If you're trying to run a keymapper to use a gamepad for Minetest then no, I don't think you'd need to make any Minetest settings changes. On a similar Linux setup I didn't need to make Minetest settings adjustments for this.

I'd expect that you'd need to start your keymapper program first, map the keyboard to your gamepad appropriately (i.e. wasd would go to the left analog stick, etc), check that it's working in a simple app like a text editor. Finally, if all of that works then try loading up Minetest.