"official" means run by wizards of the Coast, so essentially the money grab. I suppose it has some benefits in terms of not getting anyone who's swapping cards there overpaying for a reproduction too.

There's no reason not to allow them. You might legitimately prohibit them if unsleeved, but in sleeves there's no difference. Tournaments that aren't run by WotC do allow proxies, though I think Star City Games limits you to 5 proxies, which isn't enough to solve any budget problems. Again, obviously, there's no reason as far as gameplay goes. SCG does traffic in used cards.

Is there a legitimate reason for collectors to value an authentic card more than a counterfeit card?

Where do you think prize support for tournaments would come from if no one had to buy the cards?