When I am tagging my FLAC files, I use DISCNUMBER and it works will with SlimServer. However on my MP3 files I am importing to Itunes, I was using TPOS and Itunes seems to be ignoring it. Should I still use DISCNUMBER in the extended tags (and then MP3Tag will save it as TPOS)?
Yes you must use DISCNUMBER
See https://docs.mp3tag.de/mapping
The ID3v2 frames get mapped to more meaningful names.