The reason for the JAA IR having most of the ATPL ground school and a few jet type ratings
wrapped up in it is that this is what 99% of students are working towards: an ATPL and jet TRs.
So if you do any kind of future "chopped down" PPL/IR and then want to do a JAA CPL/IR or ATPL you will have to sit the additional material somehow.
The alternative is the FAA system where the IR is just an IR, the ATPL is just one 2" thick book (versus about 2 feet paper thickness under JAA) and the jet aircraft specific stuff is put where it belongs: in the type specific type ratings. But this is not likely to ever come about in Europe, with its absolutely anally retentive attitude to "safety", sorting "men from sheep" as early as possible, etc etc.