I have the same issue and I do hope that the (almost) standard Vorbis comment DISCNUMBER will be integrated soon in MC to the DISC # database field.
Until then I use this expression to get a column that combines both the standard DISC # field (for MP3) and a custom field DISCNUMBER, collected from flac files: If(IsEmpty([Disc #]), [Discnumber], [Disc #]
As I use MC mostly for searching, browsing and tag editing I must be careful which field I enter a disc number value in.
I have the same issue with the standard Album Artist field which is not populated by the ALBUMARTIST Vorbis comment in my flac files, only by the TPE2 tag in MP3 files; to show a single column with all album artists I use this expression: If(IsEmpty([Albumartist]), If(IsEqual([Compilation], 1), /(Multiple Artists/), [Album Artist (auto)]), [Albumartist]). I have not bothered to combine the Publisher field (TPUB from MP3) with the Organization Vorbis comment, which shows the same behaviour. And then there is the issue of MC not being able to read/write the standard TORY tag from MP3 files (only the ORIGYEAR Vorbis comment from flac files)... But now I am getting a bit too far off topic. I hope you can have use for the expression to alleviate your issue in the meantime.