"I understood the JAR qualification (in its present incarnation) is a SEP IR. "
NO! a PPL IR is an IR on a PPL it is no different from an IR on any other licence, it can be SE, ME, SP, or MP!
The only room for scope in amending the IR is amending the ground examinations to make them more relevant; this process is under way at JAA committee level. Hopefully, this will be completed before the JAA packs up and hands it all to EASA. There will be no change to the flying syllabus.
There has been a lot of discusion regarding the DfT wishing to eliminate N Reg aircraft in the UK. The driving force behind that is not safety based, but is intended to prevent UK pilots from using a FAA IR in the UK!