They were awesomely designed to be able to handle a little substrate - no one is clearing away leaves and twigs for them in their natural environment. They can break down bones, hair, teeth and nails with their stomach acids, they can also break down some subtrate.
I've never had an issue with swallowed substrate (and I feed 40+ ball pythons a week).
What's to keep him from associating the floor with food? Now he's going to associate your hand with food every time you put him on the floor.2.wont confuse your hand with food everytime you go to pick it up
Basically, that's a myth. You aren't feeding him every time you go into his enclosure, so why should he make the assumption he's going to be fed each time?
I don't think that just rinsing the bag makes it more sanitary.3.Feeding on a plastic bag is cheaper and more sanitary because you dont have to worry about cleaning up their tank and redoing substrate and all you got to do is rinse down the plastic bag
I guess I don't find it that difficult or a pain to spot clean as needed.4.if rats/mice poop or pee you dont have to worry about cleaning that up because itll be on the plastic bag versus in the tank