Anything on Permit or Annexe II are outside the scope of EASA and so the CAA can choose to do anything it wants for those that fly them.
Yes, I can certainly see that point. It seems to me that in FCL EASA could have made revalidation experience conditional on 12 hours in an EASA C of A aircraft. In fact they have not done that and simply specified that the hours have to be in the relevant class. For most of us that would be SEP. Annex II aircraft are of course not subject to the FCL licensing requirements nor the maintenance requirements. However, there is nothing to say that an Annex II aircraft is not still a SEP, which it clearly is, so I cannot see anything preventing you building your 12 hours on a Chipmunk, Tiger Moth or RV7 as they are all SEP. Being really devilish, it seems that you could say that what we in the UK term Microlights are also SEP! If you can count hours on any Annex II aircraft then that would appear to include microlights.
The arrangement is really quite loose and in fact there is no reason why, if you fly around Australia for 20 hours with the benefit of a temporary validation to your licence those hours should not also count, even though they are not hours in an EASA or even Annex II aircraft, as those definitions cover aircraft registered in a member state of the EU.