The reason for this mess is that the IR exams are not a
subset of the ATPL exams.
They are produced by taking the applicable ATPL exams and then stripping out questions which are not in the IR syllabus.
This is an inexact process, which is why the IR question banks are only about 70-80% a match to the actual exams (I have just finished my IR exams, after working through the
entire GTS IR QB, so I know
).
One scenario where somebody might sit the IR exams, plus the CPL exams, is to take advantage of the 15-hour ICAO IR to JAA IR conversion route, plus he also wants to be an instructor one day.
But it's an awfully long way round it, and "ATPL theory" is still needed (or is handy) for some non-commercial things e.g. flying a G-reg TBM700/850.