+1 to feeding in the enclosure: My girl is a sweety and has never hissed, struck at me or even balled up. But she has a very strong feeding response - I would NEVER want to try to handle her or put my hands the enclosure when there is scent of rat about!
And, the fuss of moving her (and the possible discomfort of moving her back with a full stomach) isn't going to make them like the process. So I'd guess it might make them less likely to eat?
As I say - I am lucky to have a really chill snake. I try to put her back when she starts to only want to hide away. Also, I'd presume it's best not to let them get too cold, depending how warm the room is.