This is certainly an unusual case! So sorry to hear about it!
I am glad you had a reptile vet who was able to help you. Maybe the snake crawled up the side of the cage, and fell over onto a piece of cage furniture? They do that all the time, but if he hit something "just right" (or just wrong!), maybe it caused the injury? He is in a bigger cage than most rats / corns live in, so maybe he had a little extra room to fall? If he had a preexisting condition (maybe congenital), then maybe a small injury caused it, something that would not have caused such an injury without a prior problem? This is all just speculation - your vet would be far more qualified to hazard a guess than I am.
I agree with the others - if a corn / rat is eating and digesting properly, it is an EXCELLENT sign that they don't feel too badly. Feeding / digesting is usually the first thing to decline whenever they suffer ANY health problem. The fact that he ate less than usual (as your other snakes did) may mean he is less active, or it may mean that it is almost winter in NY, lol! Even if you keep heat on them, they usually still know!
Also, the fact that he can move normally throughout his body, and that he doesn't seem to have any pain or impairment other than the protrusion, bodes very well for his recovery, in my opinion. I believe you said that you moved him to a smaller cage. Just on the slim chance that he is prone to falling and injuring himself in the future, it might be good to keep him in a shorter cage, and only allow climbing while out and supervised by you.
BTW, my own experience with pain in snakes is kind of strange - on one hand, if I have to pinch their tails a little, perhaps while removing dead skin, they seem very sensitive. OTOH, if I pinch a tail in deli lid (I feed all f/t pinks in deli cups, and OCCASIONALLY have caught a tail - yuck!) , while they may thrash around for a minute or two, just as often they quietly EAT their pink, and patiently wait for me to come and release them, without any sign of pain.
When I have had to use a large gauge needle to aspirate egg contents, the females will sometimes flinch a little, but very often, they hardly seem to notice. I have seen various wounds over the years, and the snake usually does pull away when it is treated, but they often don't seem to react as strongly as a mammal does with the same type of wound.
Sure hope your snake does well, and comes out with nothing worse than a minor cosmetic imperfection. Keep us updated, and let us know if the vet has any new info for you. Good luck!