When you're moving a snake from his feeding box to his enclosure, you are moving the snake - not "handling" the snake. You make it so that it would be as close to the same amount of movement as if the snake was moving from outside his hide to inside his hide after eating.
If you have an enclosure like this:
You can't really feed inside the enclosure because a rat can hide in areas that are in-accessible to the snake and taking apart the enclosure for feeding is not practical.
So yes, it is completely dependent on your set-up and your snake.
Either method is fine.