I think there is a good use case for exposing a custom URL mapping via Nginx that doesn't necessarily go to a container on the local system.
This has use cases for a single (sub)domain providing proxy and load balancing services, as well as cluster management down the road.
As of now, the default nginx.conf loads all .conf files from applications/ directory.
Unless there is anything in the code that wipes out all conf files instead of only individual ones, adding a custom on there for a custom use case won't cause problems for other apps and won't be overwritten on upgrades.
If you want to feel safer, keep the custom .conf elsewhere and use a symlink from the applications/ directory.