How to get ECK APM to work with any type of agent at all!?!

Please refrain from swearing at my colleague, and in these forums in general. I understand your frustration, and the documentation certainly needs to be improved. We'll take that on board.

Here's a script which deploys ECK, Elasticsearch, Kibana, and APM Server, and extracts the APM secret token and CA certificate.

#!/usr/bin/bash                                                                                                                   
set -e                                                                                                                            
                                                                                                                                  
# Install the ECK CRDs                                                                                                            
kubectl create -f https://download.elastic.co/downloads/eck/2.9.0/crds.yaml                                                      
                                                                                                                                  
# Install the ECK Operator                                                                                                        
kubectl apply -f https://download.elastic.co/downloads/eck/2.9.0/operator.yaml                                                    
                                                                                                                                  
# Create an Elasticsearch cluster                                                                                                 
cat <<EOF | kubectl apply -f -                                                                                                    
apiVersion: elasticsearch.k8s.elastic.co/v1                                                                                       
kind: Elasticsearch                                                                                                               
metadata:                                                                                                                         
  name: quickstart                                                                                                                
spec:                                                                                                                             
  version: 8.9.1                                                                                                                  
  nodeSets:                                                                                                                       
  - name: default                                                                                                                 
    count: 1                                                                                                                      
    config:                                                                                                                       
      node.store.allow_mmap: false                                                                                                
EOF                                                                                                                               
                                                                                                                                  
# Create a Kibana instance                                                                                                        
cat <<EOF | kubectl apply -f -                                                                                                    
apiVersion: kibana.k8s.elastic.co/v1                                                                                              
kind: Kibana                                                                                                                      
metadata:                                                                                                                         
  name: quickstart                                                                                                                
spec:                                                                                                                             
  version: 8.9.1                                                                                                                  
  count: 1                                                                                                                        
  elasticsearchRef:                                                                                                               
    name: quickstart                                                                                                              
EOF                                                                                                                               
                                                                                                                                  
# Create an APM Server.                                                                                                           
cat <<EOF | kubectl apply -f -                                                                                                    
apiVersion: apm.k8s.elastic.co/v1                                                                                                 
kind: ApmServer                                                                                                                   
metadata:                                                                                                                         
  name: quickstart                                                                                                                
  namespace: default                                                                                                              
spec:                                                                                                                             
  version: 8.9.1                                                                                                                  
  count: 1                                                                                                                        
  elasticsearchRef:                                                                                                               
    name: quickstart                                                                                                              
  kibanaRef:                                                                                                                      
    name: quickstart                                                                                                              
EOF                                                                                                                               
                                                                                                                                  
# The APM secret token is stored in a secret named "<name>-apm-token".                                                            
export ELASTIC_APM_SECRET_TOKEN=$(kubectl get secret/quickstart-apm-token --template '{{index .data "secret-token"}}' | base64 -d)
                                                                                                                                  
# The CA for APM Server's TLS certificate is stored in the secret "<name>-apm-http-certs-public".                                 
export ELASTIC_APM_SERVER_CA_CERT_FILE=$(mktemp)                                                                                  
kubectl get secret/quickstart-apm-http-certs-public \                                                                             
        --template '{{index .data "tls.crt"}}' | base64 -d > $ELASTIC_APM_SERVER_CA_CERT_FILE                                     
                                                                                                                                  
echo                                                                                                                              
echo "Elastic APM configuration:"                                                                                                 
echo                                                                                                                              
env | grep ELASTIC_APM_                                                                                                           

Running that you should end up with some output like:

...
Elastic APM configuration:

ELASTIC_APM_SECRET_TOKEN=p7x1C6aV6MtrC1I77Ly53G7w
ELASTIC_APM_SERVER_CA_CERT_FILE=/tmp/tmp.qRzQI9X0q8

To test, you can connect to APM Server from your host by port-forwarding to apm-server and using curl. e.g.

$ kubectl port-forward service/quickstart-apm-http 8200&
$ curl --resolve *:8200:127.0.0.1 --cacert /tmp/tmp.qRzQI9X0q8 -H "Authorization: Bearer p7x1C6aV6MtrC1I77Ly53G7w" https://quickstart-apm-http.default.apm.local:8200

Where should I mount the generated self-signed certs as k8s secret!?!

You'll need to mount the secrets in the pods running your instrumented applications, i.e. in the pod spec for your Node.js application. How you configure your application pods is naturally outside the scope of ECK -- you can use standard Kubernetes features to do this, referencing the secrets generated by ECK. See the script above for the secret names.