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Only an idiot would put a different set of wheels into a bike that's got crap, pulsing or squealing brakes though.
If you're fussy, you could simply swap the pads when you swap the wheels (I have to do this with my TT bike because my training wheels are alu and race wheels carbon and that's way more of a pain than swapping disc pads)
I don't bother though. As I've said, I've had no issues with swapping on the fly and until someone tests this stuff on a test rig and measures the impact, I'm not buying this accelerated wear chatter (pun intended).
What makes rotors/pads more likely to get contaminated/glazed when switching wheels on a bike? Genuine question! Is it because if one or the other gets fucked up, it'll write off the other set when you switch as well?