It's really a matter of personal preference, number of snakes, and amount of decor in the enclosure. I feed my girl in a separate box because I never want her to have a reason to think my hand would be a meal when she's full grown, and her home tank decor gets in the way anyway since she eats live. I tried feeding her in tank and it scared her silly since the mouse was grabbing for everything it could (I keep the mouse on tongs by the tail for better control). Even when I released the thing, she hid from it. Only when I moved her (after removing the mouse and washing up of course) to her 'cafe' did she relax and sure enough she grabbed that self same mouse when I dangled it in.

Naturally, people with lots of snakes to feed aren't going to take them all out, that would take too long. So for them feeding in the enclosure is much easier.
As for regurge...there's not really any danger as long as you make sure the food item is totally swallowed, you pick them up carefully supporting the now largest part of the body, and you place them gently back in their home right away. I just finished feeding Nagini, in blue, with no problems. She just slithered into her hide like always.