I mean the short answer is that operators will have to find a way of being compliant with both - if the two are in conflict I agree there is confusion.
I'm not sure how much of an issue that really is though, I fly both UK and N-reg aircraft in Europe and as long as one complies with whichever set of rules imposes the higher requirements, you are OK. I've yet to come across a scenario in which the two are in conflict to the point that compliance with both is impossible.
Leaving aside that issue though, it has always been the case that states may apply rules to the aircraft of other states when flying within their national boundaries - the fact that the origin of those laws comes from the EU does change that - it is still the law in those member states as if passed at national level.
I suppose this point could be debated for ever, we'll just have to wait and see I guess...