I think you are confused how this works. It doesn't matter what setting you use on the Yamaha, you're still using the Emotiva unless you're physically disconnecting your speakers from it and just using the onboard amps in your receiver.
I think you're talking about what Marantz calls "pure direct", which bypasses all dsp and sound processing. In which case you either prefer some dsp or you don't, and that's the difference you're hearing.