Thanks for sharing the code. It looks like you're not calling start() on the APM agent until after a lot of the imports have been called. That means that the agent will not have a chance to load before the rest of the app have loaded. And this in turn mean that it cannot add its hooks to get notified about database queries etc.
As far as I could see this project is actually based on Express, which means that we should support automatic naming of transactions. The reason why it's not working is probably the same as described above.
If you move the call to import 'elastic-apm-node/start' up to either be the very first thing in src/main.ts - or maybe even simpler start node with -r elastic-apm-node/start instead of importing elastic-apm-node/start in the source code - that should fix the problem.