I apologize, I understand your question now.
Currently at the moment the overlay container is a great tool in development for quickly testing device tree changes without having to recompile and deploy a new device tree binary. For production however as you’ve noticed it gets a little bloated with having to pull/deploy/delete this container on each SOM.
In the future we plan to have better device configuration integration such that these changes can be easily deployed in a production environment.
For the present though the overlay container is more of a development tool for figuring out what changes to the device tree are required. In the end it would be best to have this changes patched into the device tree proper, that way they are even then picked up by our OTA update system.
I hope this helps better answer your question.