I have fed a snake in a separate enclosure for almost two years now. Partially because of substrate worries and partially because her enclosure is too freakin high up! I can't reach in well, and if something went wrong I couldn't get in there to help. So we feed her in a spare ten gallon. We've always just picked her right up as soon as the rat looks settled and put her back in her cage. Never had a regurge--that happens moreso if you really stress the snake..Handling them for a couple hours or so, not a good idea. Just moving the snake isn't that big of a problem.
A lot of people question the worry of impaction in snakes anyway, though I have seen it happen before. Generally speaking if the temps are right it shouldn't be a problem and your snake should be able to pass it. But it still worries me, I'd rather feed on paper towels. She's being moved to a lower down enclosure anyway where she will be fed in the enclosure on paper towels.
Some people like to put in a paper towel or paper plate in the enclosure over the rat for the snake to eat on. Prevents any worry of substrate ingestion for you, and you don't have to move the snake after it eats.
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