That aggression you see when transferring him back to his enclosure is one reason why many prefer to feed in the enclosure. It sounds like the in-tank feeding went fine; it's normal for them to look around after 'killing' their food, just to make sure they're safe (eating puts them in a vulnerable position). With my fussy eaters I like to throw a towel over the cage after they take the food so they can feel more secure when eating. And feeding while he's in his hide is perfectly fine; it makes him feel like he can 'stalk' the mouse from a safe place.
Cage aggression (snapping at your hands when you open the cage / thinking you're food) is really not an issue with ball pythons. I have never seen a cage aggressive ball python (so long as there's no scent of food). But if you're nervous you can always tap him gently on the neck with a snake hook (a clothes hanger works just fine if you don't have a snake hook) before reaching in and picking him up, but keep away from the head because ball pythons are very head-shy and will be startled. As I said, I don't think it will be an issue, but the 'hook training' method or gloves are great to use if you are hesitant about picking him up.
I would seriously recommend feeding him in the enclosure. It is so much easier and you are much less likely to encounter complications. However, if you do want to continue feeding in a separate container, I would recommend waiting 15 minutes after he's eaten before transferring him to his regular cage.
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