I think I have most of this figured out. For about the first year-and-a-half, all Ultraverse comics had a regular cover and a UPC cover, almost always identical except for the UPC box (there are some variant covers but I think we figured those out a long time ago).

In fall 1994 they changed the box at the top left of the cover from a big Malibu logo to a smaller logo with a head shot. Mantra 15 and 16 is an example.
I think that change marks the end of the UPC variants … a few months later all Ultraverse books had UPC boxes no matter where they were sold. I have visually verified this with almost all of the UPC books.
Anyway, here is what I came up with:
UPC list
Break-Thru: 1, 2
Elven: 0
Exiles: 1, 2, 3, 4
Firearm: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14
Freex: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 (14 unverified), Giant Size 1
Hardcase: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 (17 unverified)
Lord Pumpkin: 0 (maybe)
Mantra: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, Giant Size 1
Night Man: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
Prime: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 (16 unverified), Annual 1
Prototype: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, Giant Size 1
Rune: 1, 2, 3, 4, 5, 6 (6 unverified)
Sludge: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 (11-12 unverified)
Solitaire: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
Solution: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 (13-14 unverified)
Strangers: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17
Ultraforce: 0, 1, 2
Ultraverse Origins: 1
Warstrike: 1, 2, 3, 4, 5, 6
Wrath: 1, 2, 3, 4, 5, 6, 7, 8, Giant Size 1
Those unverified ones, I’m not even certain they exist because another potential reason is that this might have been a timed change (around September-October 1994). If you have actually seen one of those, let me know!