It's doing the right thing - most of the harm has been done with the battery being charged up in the first place. If you can pull power from the wall instead of battery, do it. Ordinary usage will chip the battery down to the charge limit in due time.
I have an ASUS laptop which does not do this. When you turn on the battery limit, it stops pulling power from the wall until the battery is down to the right place. Very rude.
Steam should be loading a separate controller config for every game, or at very least loading a default profile of "every button is literally the same as on an Xbox controller". A weird SteamInput config shouldn't affect across all games, I think.
Does it act up in Desktop mode? How about if Steam is closed, and you play something from Heroic?
It's possible that a hardware fault is sending insane inputs. Bad connections to the controller-sub-boards? The controller microchip just going batty?