The problem could be solved by placing PCM audio into some other container format. WAV proliferates for historical reasons but perhaps we need a slightly more modern audio container format that will accept any kind of bit stream + metadata, etc. I suppose MKV could fit the bill today. Are there any other good candidates?

It can - it has supported RIFF INFO from the start, and ID3 support exists.

If software writers choose to not extract metadata from WAVs that's up to them... but I guess it amounts to the same thing if you only want to use software that doesn't read tags in WAVs.

In a pinch you can play FLACs using the built-in Files app, actually. Still better off using a different playback app for any long listening, though.