The 'dark' ages are a myth (at least in the way we think about em) but I'd actually say modern historians are pretty good about dispelling that. If anything I'd argue that the Romantics were the ones that started throwing the term around really and that recently modern historians are actually much better at seeing past that. As for modes of thought, I dunno actually. Yeah you had a particular set emerge in Europe during this time but it would be rather silly to think that European thought alone emerged as a victor in the modern day (there are definitive parallels in most civilizations, I'd say, and they tend to appear in very particular time-periods). What I mean by that I suppose is that globally there are different strains of a sort of 'progressivism' (if you want to call it that - ideological breaks from the past) which are not really linked to Europe, and certainly didn't appear in the same context.
It's complicated, though -- you can trace the European dark ages (such as they were) through archaeology. Read an amazing book about that once but it had a generic title that I can't recall. So yes and no. I disagree with your second paragraph.