R-N402D is dead silent when you use it's DAC and not so trough analog inputs (and neither is the rest of the line with possible expection of A-S700 and R-S700 in economy class). YPAO ain't great and there is a considerable performance degradation when using it. Did you considered going with something like MiniDSP Flex or Flex HT instead? By the way R-N402D perform the best when you feed it 2V (or with it's own Burr Brown) and set the Volume Trim to - 7 as I have one. No automatic room correction will cope very good with beeming under and room modes (as it simply doesn't translate good to room ringing) so you can do it much better yourself with trial and error trough multiple PEQ passes. Future more one sub out or chenel and one sub won't do very good if you need a crossover over 80 Hz (you will be able to pin point from where it comes), for that you need pair of sub's and 2.2 setup (which ironically doesn't exist from manufacturers). What does exit are multichannel DAC's/DSP's in various forms and such so you make one do 2.2 output.
I am INDEED using its own internal Burr-Brown : I Use the Yamy CD-S300 as a pure transport, it then goes through the NanoDigi for RoomEQ, Then into the Coax DIGITAL of the R-N402D. That one does the whole D2A conversion in the process. When Streaming, I use a PC running Qobuz through Audirvana and a VST3 PEQ plugin over the network, so it's all done in the digital domain too.
On the Sub side, I'd favour the R-N803, because it has thas BOTH a dedicated Sub Out AND a 12v Trigger out, which I find very convenient. Gives you more option. Currently, my sub is Hooked to Speaker B Terminal. Convenient to cut the bass at the touche of a button if needed, but still the sub is powered. MusicCast allows you to set the crossover from 40 Hz up to 200 Hz, so I guess you're covered here. No multi-subs indeed, but many AVRs have fake 2.2, i.e no 2.(1+1) but 2.(2*1) : two sub outs, but one and same signal.
Finally, Thanks to Amir, we have good measurements for the 803, none for the 402. I suspect it's decent, and I would probably keep the 402 if it was better, but I can repurpose it, and see what YPAO does by measuring it, then if it's valid, tweak it to my taste.