There is clearly a difference in the 2 autopen signatures. Does use of autopen require a documented signature, so there should be a record of the signature changing, and I would also think anytime the autopen is used it whoever used it would have to be documented.
My guess is the later autopen signature was made by Jill. Perhaps Joe could no longer sign his name, or he refused to sign.
I think whatever happened with Biden stepping down it was done with Jill's approval, forced or otherwise. It is questionable who had control of the autopen which caused the need for a second signature to be recorded.