I have to say that I much prefer a digital signal. The AV amp then does all the decoding raw with less error correcting because of a muddy signal reception.
In theory, with digital signal, there should be no difference in the output quality regardless of the input signal, all things being equal, because the processing is done by the same device.
I have spent hours listening via both inputs and couldn't hear any difference. That said, I would not call myself an audiophile, the type who can discern the slightest audible change in a layer of sound or frequency. I'm more of an enthusiastic amateur who knows how things are supposed to sound and what he likes.
In the end I chose to go with HDMI out into HDMI in on my amp. Nice and tidy behind the system, well relatively. But with all things audio, it's very subjective what is good for the goose may not be good for the gander. I would just say have fun trying both of them out until you decide what suits you and your ears best.