yes, play clean chords. you will still be able to palm mute and chunk once you finish the tonematch. playing clean chords just gives the axe-fx more tone to work with, which makes it more accurate.
Nope. It would actually be harder to match a magnetic-pickup tone if you're using a piezo.I imagine you would need to have a neutral type pickup (piezo) for this to work somewhat reliably. That is what the Variax does. I've got a JTV 69 Variax on the way. I can't wait to get it.
If you guys like, I'll upload some dry recordings of my '59 Les Paul clone (with Seymour Duncan Antiquity pickups) as well as my Standard Strat (with DiMarzio Area 58/58/61 pickups).