Is it the way Yamaha wrote the software?
When I run YPAO on my 5 year old RX-A1020 it sets the front and rear surround speakers to Large, side surround to Small, and Center channel to Small. Subs it sets cross over to 150Hz.
I end up manually setting all speakers to Small and subs at 80Hz crossover.
All speakers are bookshelves, not towers!