How to clear specific keybinds?

I have a NES-style gamepad with two face buttons (one less than in the embedded image), a D-pad, ‘select’ and ‘start’. The issue with Shovel Knight is that the game allows duplicate keybinds seemingly without limitations and I can’t for instance avoid sharing the ‘pause’ function with some other action due to how the defaults are set.

The easiest way I know to sidestep the issue is to access the inventory using keyboard instead of the controller.