I cant even imagine how that would work. But if I can figure out a way to present it in a decent manner then, sure, why not?

This has just been added in the latest version, you can now change character marks from MCM.

Unrelated but is it fully compatible with Unintrusive Pause Menu? For Vanilla characters the marks are placed just fine on the right like in UPM screenshots, but with modded characters, sometimes they are not there, sometimes they are there but still on their default place and weirdly red with monochrome outlines, and sometimes they appear when I restart.

Not sure if it's an incompatibility, cause I use UI mods like Re-color (but they don't edit the marks I think)

Thx!

The way you see the marks look is on them, they used to look in the transparent fashion you are seeing but they seem to have updated the mod partially and left the old marks in there for whatever reason?, I dunno exactly what they did but for as long as they replace the marks sprite with the transparent one, you'll see it that way with their mod on, theres not much I can do about it.
Now, I just pushed an update that changes the position of the marks on the pause menu to be closer to the position they use (it will be lower but I think it obstructs the view more that way). I have no clue why the marks wouldnt show up tho, if you face that issue again tell me which character you are playing as and check the log/console for errors.

The completion mark sheet disappears slightly out of sync of the pause screen

yea, not much I can do about it. It disappears when the game is unpaused, but the menu starts closing before that fact.

Completion mark sheet appears on boss transitions

You mean the tab one?, because if you hold tab while entering a boss room then I think I'm fine with it showing it. If thats the case, I would appreciate some enlightment as to why would anyone do that? (if you actually have a reason I'll look into it).