Just read your edit:
if your son fusses/cries when he is in the corner. Try just letting him be. Maybe he will be fine, and go back to sleep. Unless his "cry" escalates into screaming and totally waking up. Babies do make noises anyway, while sleeping. So figure out his noises... and which cries actually means it is warranting intervention, or not. Some babies just scoot around their crib when sleeping... and it inevitably means scooting toward the direction of their head. Because their legs are scooting/pushing "up." Thus they get stuck, at the top of the crib. Maybe try position him lower down in the crib... so when he scoots around, he will not end up in the corner of the crib. ?
Is your son actually waking up, because his head is in the corner or his crib against the bumpers?
If not, I would not bother him, waking him up, and just let him be. Not readjusting him. Because maybe "that" is what is waking him.
Bumpers are fine even now. I have always had the bumpers in my kids' crib... and never removed them. It never caused a problem.
You do not have to get up/wake up, just to move him/readjust him, if he is sleeping fine. He probably just likes the coziness of being up against something... and finds it comfortable.
With both my kids, we also had baby safe stuffed toys in the crib with them, too. And my kids had a lovey.
all the best,
Susan