I'm not sure the TCM has a flash counter, I believe instead that they can tell because something in the flashed data is a giveaway. BNR would need to specify as they didn't in my email exchange with them on the subject, but they seemed specific to NOT mention a counter with the TCM. It could simply be that the adaptive learning is permanently disabled in the flashed TCM, which it would never be in the stock TCM programming, for example.
Unfortunately a lot of this stuff isn't very well documented (clearly/definitively) by the mod developers. I'm sure they have their reasons.
Yes, no transparency needed for the 1.8L since there's no flash counter.