Most of that post makes little sense to me. I'm confused as to your issue. You shouldn't really hear any differences in sound quality between the Yamaha and the Emotiva. Switching sound modes will change the sound, of course, but that has nothing to do with the onboard amps over the external one. It's just a different sound mode. It's going to sound different.
I personally only listen to music in stereo. Some stuff is meant for multichannel and some is meant for stereo. There's some wiggle room in between and some folks do like listening to stereo in 5.1 but it's not for me.
Leave it set at 8 ohms for sure. The lower setting cuts your power to accommodate lower resistance speakers. You have an amp shouldering some of the load and the 2080 is pretty capable on its own.