On all platforms that have a VR compositor available, we push textures into that compositor as overlays so that the game doesn't have to render at framerate while loading and players still have something interesting to look at (including progress that updates during loading). Since our upgrade from Unity 2019.4.23 to 2020.3.12 this no longer works on the Quest (it still works fine on Windows Oculus with a Rift or Link, and also on SteamVR but that's an entirely different codepath).
Interestingly, in a simplified test-project that uses the same approach to push the overlays into the compositor, this works just fine. But when I copy those scenes / prefabs over to our main project, and do a build, the overlays do not work in that build.
I have compared the project settings and manifest.json and it seems that there are no difference that should cause this.