First off, let me say that feeding in a seperate container isn't a bad idea as long as the snake isn't a nervous snake that's handled too soon afterwards to where it regurgitates. Some snakes don't have any problems being handled right after feeding but some do. Its best to use a hook to put it back in it's cage.
Now, with that said, I'll say this; there are many ways to condition a snake not to expect food from a hand in its cage. The only reason I've ever feed one in a different container was due to the substrate, to avoid the snake swallowing it while eating. This was in a display setup.
I feed my 10ft & 8ft burmese pythons in their cages. I've had them since they were babies and have always done so, without a single bite or strike.
At feeding time, I open their cage, stroke them a few times with a snake hook, get them out and handle them for a while. Place them back into the cage & feed them. I use 3ft long tongs to feed them so they never see my hands.
I've got a 4ft corn snake that I sometimes put a rat in it's cage by hand, holding the rat by its tail and dangling it to get the corn's attention. He associates the dangling rat with food, not my hand. And this is a wild-caught corn. Never a bite or strike from it, either, and I always reach in with my hand to get the corn snake out.
If you use long tongs, stroke your snake with a hook and use the hook to remove your snake from it's cage, you'll rarely, if ever, have any feeding response strikes.
If a snake is seldom handled, other than removing it to put it in another container for feeding, wouldn't you think it would still associate the opening of the cage or being removed, with feeding, and possibly still strike?
Bottom line, I feel, is that as long as you handle your snake fairly often between feedings it will learn that a hand or the opening of the cage does not constitue food. Use a hook for the territorial ones, they usually calm down once out of the cage.
This subject has been discussed a few times recently in the Corn Snake forum. Read through some of those threads for more input, pros & cons.
Take care!
Mike
-----
It is said that 1 out of every 4 people are mentally unbalanced. Think of your 3 closest friends, if they're normal, then it's you.