The APR Plus provides a wrap-around warranty that covers any issue that your stock warranty will not regarding the engine. That's the whole benefit of APRplus. You get less of a power increase, but you can finance it with your car and you still have an engine warranty.
Also, most other VW cars get pretty large increases from APRplus. I don't know why the GOlf R is limited so much -- it might have something to do with preserving the drivetrain or something.
And for the other confused people, APRplus is a "lower" stage than APR Stage 1. THing of it as a dealer-installed "stage zero" that comes with a warranty.