While I agree you want to primarily adjust in the AVR, I don't think the sub should be at 50% gain, it should be around 75%. I would also say run YPAO more than once and see if it comes back with the same results. I know on my system, I ran it 3 times and 1 was different from the other 2, so I kept the one that came back the same and adjusted from there.
The adjustment takes into account not just the volume, but also the distance away, to create one setting that balances both. Check to see if it set your other speakers large or small, I find mine often sets them to large when it shouldn't.