There's a bit more to it than that.
Kibana's data security is entirely dependent on Elasticsearch's security model. If you want to view data in Kibana, then you need to have access to that data in Elasticsearch.
The only user that we ship that has out-of-the-box access to data is elastic.
This is a superuser that can do everything.
You can use that user for everything you want to do, and always login to Kibana as elastic, but we don't recommend it. Because that user can do everything, it can make a horrible mess of your cluster if you're not careful, and one of the benefits of X-Pack security is that it can protect you from mistakes like that.
Rather, we recommend that you use the elastic user to login the first time, and then use the Kibana admin screens to create new, lower privileged users and roles that have just the permissions that you need, but nothing more. You can then safely use those users to do your work in Kibana, and you can always login as elastic if you need to make major changes.
some of the indices have yellow health
An index is yellow if all primaries are available, but some (or all) replicas are missing.
It looks like you have a single node in your cluster, so it is not possible for the cluster to assign any replicas.
By the way Kibana continues raising timeout errors on every start
This is strange, but it doesn't seem to be causing any real problems, so I don't think it's anything to be worried about. You could ask in the Kibana forum if you're worried.