Curious indeed! The Agency has stepped back from its previous position, where it did not acknowledge any experience in Annex II aircraft, but only as far as allowing experience in microlights to count towards the LAPL requirements. The amount of credit that will be allowed for this purpose will be decided by the ATO providing the training on the basis of a pre-entry flight test. However, no other credits will be available (e.g. for issue of a PPL, CPL or ATPL or revalidation of a type or class rating, FI certificate, etc.). You are, therefore, correct that any time flown in a Chipmunk will not count towards the revalidation of an EASA SEP class rating.
EASA's repeated mantra in the CRD on Part-FCL is "Aircraft included in Annex II to the Basic Regulation are excluded from the scope of Community competence; therefore, they are excluded from Part-FCL."
The regulation of Annex II aircraft will be the responsibility of individual member states, who will determine their own licensing requirements. Should a state choose to use the EASA licence for Annex II aircraft (which I expect most will do), it will be able to enter a 'national' rating in the licence, just as the UK currently do for the Finist, Jetstream 100/200, etc. on a JAA licence.