When I was in the UAS a lot of years ago, you flew the UAS syllabus regardless - but the hours I got certainly went towards my eventual JAR-PPL(SEP).
However UAS now I believe is far more about the officer / adventurous training aspects, and I suspect that they're rather more flexible over how the flying hours are used.
But, they're paying for the flying, so they decide what you do, or don't do with the hours!
G