First off...don't panic. Do you think they get fed in sterile plastic tubs in the wild? Their digestive systems can handle twigs and other small foreign objects. Some snakes can go weeks between poops...especially if they are young and growing. And they're not always regular as clockwork. Sometimes they poop more often, sometimes not.
You might try a soak in a shallow tub of luke-warm water...water that does not feel either warm or cold to the touch and is only deep enough to come about halfway up the sides of the snake. That often prompts a bowel movement. But either way...I wouldn't worry about it and go ahead and feed as planned.
If feeding in a separate container worked for you and you were comfortable with it, there's no reason to not continue doing so. If the snake doesn't care, and you like the routine, there's no reason you HAVE to change it. But if you like the idea of the convenience of feeding inside the enclosure...there's no need to let this put you off of it.
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