what do you mean?
CoverArt is normally the "cover" ie the CD cover of Vynl sleeve of the album. So if it is a compilation, then that is what you are getting.
If you mean, can it instead use a non compilation, non greatest hits, cover from a single-artist album which that same track as also appeared, then I would really like to know ANY program that can do that.
If it could also just use 500x500pixel jpgs no greater than 80k in size and embed into the flac/mp3, then I would be game too! :-D