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Typically you'd name the extension ".mka" then. Any reasonably modern player using ffmpeg libraries for decoding should be able to deal with them fine.

Fun fact: There's also ".mks" for only including subs.

https://www.matroska.org/technical/codec_specs.html - it seems that .mka would be perfect, it supports all codecs basically, and so you can losslessly move audio into the container and back out if needed.

You still need players that would understand how to display subtitles for a .mka container.

I've had no issues using either mplayer on *nix, or foobar2k on windows for audio-only MKV.

Yea they can, MKV is just a container. If you open up MKV container via MKVToolNix, Handbrake or MediaInfo, you will see various formats in there. Though, not all audio/music players have a support for MKV and its variant.

Probably, I know I could create an MKV file with only Blu-Ray subtitle tracks (I archive the original when ripping my own stuff) and it was actually stored as a MKS. So I assume the same can be done with audio.