The woofer is what benefits from the external amp, I'd done a side by side with one speaker connected to a 4520 and the other with the amp. Bass was the most audible difference. The DAC's in the Yamaha are the finest I've heard, there is a noticeable fidelity increase. Whenever the day comes for the 'ultimate', I see the value in something like the CX preamp, it has the upgraded DAC on each channel, not just the front like the 3060. But I'm a long way from upgrading my surrounds.
I haven't tried YPAO, I prefer manual setup. Just been enjoying the Phil's in stereo lately, and yeah pure direct sounds nice!