same category of aircraft (e.g. helicopter experience does not count towards an aeroplane licence, etc.)
Not only is that a bizarre interpretation, but I am unable to find anything in the regulations which supports it. Where is the regulations is this distinction drawn? "Category" as far as I can see is unrelated to whether it is Annex II or C of A and the EASA comments in response to consultation appeared to confirm that, for the purposes of qualifying hours, flight on Annex II aircraft would count. I assume that is what you are referring to when you mention the CRD, but I cannot see what FCL changes you are referring to.
Revalidation by experience is not specifically mentioned in Part FCL in terms of the maintenance regime the aircraft has to fall under, but it would be strange indeed if the qualifying hours for say a CPL could be on anything but the 12 hours for revalidation by experience had to be on an EASA SEP for a SEP class rating. What then of the minimum take off and landings to enable you to take a pasenger? Is it suggested that these have to be in an EASA aircraft in order to take passengers in a Permit aircraft?
The regulations are completely silent on the question and "category" is nowhere defined by reference to C of A. An aircraft is a SEP irrespective of which maintenance regime it falls under if it has one piston engine. The distinction between helicopters and aeroplanes is not the same point and that I think is clearly covered in the draft FCL. Revalidation by experience always depends on the accurate keeping of the pilot's log book. In many cases you may not easily be able to gauge whether the 12+ hours in the last year were on an EASA or Annex II aircraft, as that information is not generally maintained in a log book. As an extreme case, take those types some of which are on a Permit and others of which are on a C of A, like a Pitts S2A or a Bolkow Junior. This aspect is quite unenforceable if this interpretation is right.