My twopennorth:

1) It's not the riders fault they more than likely are not aware;
2) It's common knowledge that combining internal parts (crank etc.) from different models of ZXR gives a bigger cc engine (as run in the TT quite legit. by Blair Degerholm for one);
3) Last year some teams (that I spoke with) expressed dissatisfaction with a perceived inconsistency and advantage held by the XR69s which are not 'period' (arguably by some but I would agree they aren't albeit I really like the bikes) v the later mono shock bikes e.g. ZXR, RC30. 
4) Rumours were also about last year that at least one of the ZXRs was oversize and that if the Classic TT is a 'show' race where rules can be flexed then the other teams running ZXRs might as well follow suit to at least compete against each other if not against the much larger cc XR69s.

So my speculation is that in anticipation that a big engine would not be a problem more teams opted to build one this year then were caught out by a change in scrutineering practice. If Mistral are correct in the assertions they make on Facebook then inconsistency remains. It seems hard to ask teams to guess if the rules will be applied or not or how?

Let's not forget the Mountain course is unforgiving and it takes a huge cost, effort and courage to race it, seems to me only respectful to be clear where everyone stands.