I've done a couple woodrail/prewar BGs and I did notice one time that the TT softened that black mask. It was like the solvents kind of reactivated it. I left if be and once fully cured seemed to be ok.
I only found out it softened the original paint because I was spraying outside and a small bug got stuck on glass. I used a blade point to carefully lift the bug (should have just left it in) and when I barely touched black, I noticed it was smeary. Luckily it was a tiny spot and I left it be after that.
The next time I used TT on a BG of that era, I did a couple light sprays to hold lose paint, did a couple medium coats to seal it all, then left it alone to cure for a couple days. No problems.
As far as how to address large paint bubbles that are there to start with...well, I don't have any better an answer. Mine were kind of already flaky, so I sprayed to keep it from getting worse as best I could.
Have had bubbles on a couple more modern BG and I didn't pop or flatten them. I sprayed over them which means they won't flake off, but if you pressed them, they would probably crumble. Does concern me leaving a bubble like that as I have wondered if the bubble could get bigger without being stuck to glass (as mentioned), or...is the TT over entire glass ridged enough to keep paint together even not stuck to glass....
Mostly, I think EVERY case is different :/