So am I correct in assuming the rubbing is on the right side - like if you hold your thumb up like you're giving someone a "thumb's up"
- that side? If that's the case, I would say it's possible that your right lateral pitch is probably off, that is, assuming your thumbhole is snug but not tight.
I would also say that a thumb slug or insert would benefit you. It's tough to go from somewhat slick to grabby right before your thumb exits the ball. That would be #1 to fix so start there.
#2 would be to make sure the thumbhole is not too tight. I think the majority of your thumb problem happened because of the tight thumb hole and thus having to jam it in. What I usually do with oval thumbs is measure both the thin and wide parts of the thumb, drill one size larger than the thin measurement and sand out the rest. If I have to run a sander like crazy, then I do it. I also teach the bowler about the virtues of tape and how to use it and how to apply it.
#3 would be to make sure of the lateral pitch once you've found a comfortable fit with your thumb. Monitor any sort of rubbing on that side of your thumb. And more wear on it and that would indicate too much right (under palm) pitch.
First and foremost, though, get a slug or insert for that thumb. Have the ball drilled and finished to accommodate that callous and (hopefully) as it begins to shrink (which might take a month or so), replace the slug with a newer one that fits better and still snug, not tight.
I've seen worse than yours - about 2 of them - and I've managed to correct them and return their thumbs to near normal size. Once you correct the problem, then drill up your NV. Until then, put the NV aside and make sure you find a proper fit. It won't hurt for it to remain blank for a little while. That's what I've done with my Wrath that I plan to drill up left-handed. Until I find a grip I like, I'll butcher the ball I'm using. This way I don't screw up a better ball.