I have two Yamahas, RX-V2700 and RX-V3800.
You're correct.
The "front" routine leaves the mains untouched, and sets the rest to match the fronts.
I also ran all three, front, natural and flat, and saved each one to a memory slot.
Toggling amongst the three, on my system, and in my room, natural sounded best.
And of course, from there we can tweak what YPAO did, and then save that to a memory slot. This way, the original YPAO results can be reloaded if need be.