I don't know if it's the same for ball pythons as other snakes... but I feed my other snake in a separate container. She was super defensive when I first got her, and was told she was fed inside her vive. She has settled CONSIDERABLY - to conclude that her positive change was because of that one factor might be inaccurate, however. It could have been a number of things.
I don't handle her after feeding, but instead place her container opening inside her vive until she climbs out. I don't know if that would be possible for some of the larger snakes though, or smaller-opening enclosures.

I do plan on using a separate container for my ball python when I get him (hopefully him), and see how that goes. Although I do agree that you don't want your snake to associate being taken out with feeding, I also do not want my snake to think that me opening the lid is associated with feeding. I think if you handle your snake consistantly and appropriately, they should not associate either with feeding - regardless of where you feed them.
I personally do not have a large collection, and prefer to clean, change water, etc. while my snake is out also.

As long as your snake is happy and eating (and not biting you constantly), I don't think it matters where you feed them.