Sorry, no clear answer from me, just food for thought!
I have looked at the RN 803, and it is an interesting unit.
On the positive, there will be no Video settings to clutter the menu as you are setting things up.
On the neutral, I believe you will still have the same routine for audio setup as you do with the AVR - a lot depends on how much time Yamaha put into simplifying YPAO when they adapted it to a 2 channel receiver. Ideally the surround options will have disappeared from the manual and the display (rather than being grayed out).
On the negative, the 803 has no video connections so you lose the benefit of on-screen display! I have setup a Marantz AVR for a 2.1 system without OSD, but it involves having the manual in front of you so you can successfully navigate the menu structure.
So, IMHO, if Yamaha decided to rework the software from the ground up to adapt it to 2.1, I think you will realize your objective. However, if they did not go through and remove all of the "extra stuff" from the user interface, there will be marginal benefit (or a loss due to no OSD)!
Have you listened to your current setup with and without YPAO?
If you don't need YPAO (and especially are getting a good tune out of your subs without it),I'd either get the refurbished Onkyo TX 8270 for $350 (msrp $600) which has a variable crossover with settings ranging from 40 to 200Hz:
https://www.accessories4less.com/make-a-store/item/onktx8270/onkyo-tx-8270-2-x-100-watts-networking-a/v-stereo-receiver-w/hdmi/1.html
Or the Outlaw RR2160 for $780 (Black Friday pricing through 11/27/18) which has a simple switch on the back for 60, 80, 100Hz, or by-pass:
https://www.outlawaudio.com/mofcart/blackfriday2018.html
I have not really done a thorough review of the features, but I'm not sure, aside from YPAO, what the 803 offers that these do not.