What is the problem you are facing?
Ability to listen to music stored in a way where entire CD is stored in a single audio (flac/wav/ape/tta etc.) file and track information is stored in a CUE file (external or embedded to the audio file).
What are the possible drawbacks or issues with the requested changes?
Supporting CUE can be PITA and very few players actually support it and even less support it fully (i.e. importing to media library, playlists support). You'll have to somehow stream part of a file instead of entire file, not to mention store in library a "track" that is a pointer to a fragment of a file.
You can look at how MPD https://www.musicpd.org/ handles it, but it's a bit of barebones support - cue sheets act as special playlists, tracks aren't imported to library and playlists containing the CUE-split tracks become somewhat broken upon load.