I've been thinking about this recently too, mostly to figure out how to preserve indexes in tracks of "Murmurs of Earth"[0]. I think the FLAC embedded cuesheets could be used for this. While intended for CD-ready cuesheets embedded into one big FLAC, there's no reason they couldn't be used in individual files, with index 00 for pregaps.
I'm not sure it's well supported anywhere however. Maybe foobar2000?
Edit: I pulled up the RFC[1] for FLAC, and it seems like this is a use case they had in mind for the embedded cuesheet:
> A cuesheet metadata block can be used either [...] or to provide a mechanism to store locations of interest within a FLAC file.
I'm not sure it's well supported anywhere however. Maybe foobar2000?
Edit: I pulled up the RFC[1] for FLAC, and it seems like this is a use case they had in mind for the embedded cuesheet:
> A cuesheet metadata block can be used either [...] or to provide a mechanism to store locations of interest within a FLAC file.
[0]: https://www.discogs.com/release/6057232
[1]: https://www.rfc-editor.org/rfc/rfc9639.html#name-cuesheet