some internet engineers say to use one guitar for all the rhythm tracks to avoid intonation differences. not sure how true that is, given different guitars with same scale length properly tuned and intonated. but I generally follow that advice and get the tone differences between the rhythm tracks from everything else but the guitar.
If the guitars are setup correctly intonation shouldn't really be an issue, it's the pickups on an electric guitar that make the biggest difference as far as changing guitar, string gauges and material/thickness of picks used can also change the sound slightly but it's more about attack at that point.
I like quad tracking with the same tone because it makes it super fat and focused since all the tracks reinforce each other. I feel like I lose some "power" when doing 2+2 with two diff amps.
i usually do 2 takes panned hard left ...hard right...solo up the middle...same amp sim on both....different amp or setting for solo...never use multiband..prob should...however...im finding audio assault plugings...either with wall of sound or even their cabs sound excellent....they are soooo inexpensive...im amazed at the price of some of these other units compared to audio assaults stuff...theres not much difference except the price