I only have very limited experience with custom config for Traefik.
So far i only added a custom config from the UI and followed the directions of How do I prevent the administration page from being accessible from the Internet?. Which also mentions the risk of missing persistence.
So far this has worked well, as the same time i do not think there has been any updates for the Traefik module since i implemented the changes.
So i might be in for a surprise when that happens.
Cheers.