I may be wrong on this, but my understanding is that no non-ICAO license is automatically accepted outside it's country of issue. But, the NNPL(microlights) has been around as the PPL(A)(M) and before that the PPL(D) for years. So, BMAA and it's friends have had 20 years to negotiate overflight permissions, and once various countries grasped that only the name had changed, there was no problem.
NPPL(SEP) on the other hand was a new beast and Johnie Foreigner didn't know what to do about it - probably because nobody had told him. However, from what I've seen on the PFA's website they're doing a pretty good job of setting that right.
G