Apple has (to a first approximation) a royalty-free license to ARM IP by virtue of the fact that they co-founded ARM - so yes, Qualcomm is most likely paying ARM more than Apple is.
Apple did not help them design the CPU/Architecture, that was a decade of design and manufacturing already, they VC'ed the independence of the CPU. The staffing and knowledge came from Acorn.
I believe they had a big hand in ARM64. Though best reference I can find right now is this very site: https://news.ycombinator.com/item?id=31368489
They had the Newton project, found ARM did a better job than the other options, but there were a few missing pieces. They funded the spun out project so they could throw ARM a few new requirements for the CPU design.
As a "cofounder" of ARM, they didn't contribute technical experience and the architecture did already exist.