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I do the same. I use caddy reverse proxy, and find it useful to use the container name for url, and no ports exposed
What is the benefit for making changes with separate files?
If you have relevant containers (e.g. the *arr stack) then you can bring all of them up with a single docker compose command (or pull fresh versions etc.). If everything is in a single file then you have to manually pull/start/stop each container or else you have to do it to everything at once.
This. In addition, I've read that it's best practice to make adding and removing services less of a pain.
You're not messing with stacks that benefit from extended uptime just to mess around with a few new projects. Considering my wife uses networks that the homelab influences, it would be a smarter choice for me long term to change things up.