Late reply, but yes. You can mix and match to record from Pulse but playback to ALSA too (or the other way around) but I think using Pulse for both makes more sense.

I've also been hit by .* matching ... First of all, I find this really really jarring. It makes sense and doesn't at the same time. I also wonder how to properly only glob the hidden files but I'm too afraid to experiment.

I've been using Audacity with PulseAudio for quite a while now and it works fine for me. I sometimes find myself tweaking volumes in PulseAudio on the side.