Feeding in a separate container is not necessarily the best way to go in every case. I don't feed any of my breeders or juveniles in separate containers (of course I also have way to many) but there is another advantage. For all my females, I try to hold the mouse by the tail and let the snake grab it. They almost always strike and then constrict on the prey, just the same as if it were a live mouse. This gives the snake some important exercising of the muscles, which helps to prevent egg binding when they lay eggs.
You may wonder if this practice makes the snakes prone to bite you, with the exception of a couple of particularly nasty corns, they all still behave like pussycats when I go to handle them (as long as my fingers don't smell of mouse).
Of course, if you are using any kind of a substrate that could be harmful if ingested, then I agree, feed them in a separate container.
Mark