analog bison
Your 8bitdo controller is using a controller API called Xinput to talk to the computer. The B button is quite literally the A button when interfacing with the PC, and no software can tell otherwise. You'll have to remap the controller on a per-game basis to "fix" this.
It's kinda like removing the F keycap from your keyboard, putting on the X key, and expecting the computer to know that you mean to press F.