I think you can generally assume that people won't try to mix multiple gamepads in a single input set; it seems like way too much of an edge case for the headache it would be. I know in Unity the gamepad indices can completely change around with disconnects, and I can't imagine Game Maker would be much different in that regard. (Although Unity does lack a way of directly checking the "name" (i.e. "XBOX 360 Controller") of a specific gamepad, instead only offering an unpairable list of names, so GM might have an advantage there...)
All To Get Her just stores the basic button/axis names - which gamepad IDs it checks for those depends on the mode. The game assumes that the first gamepad to press anything was Player 1, although when you're in One-Player mode, it actually takes input from any gamepad, which is what you'd probably go with for a single-player game. If you try to enter Two-Player without it knowing what ID Player 2 is yet, it asks for manual calibration (Player 1 press a button, Player 2 press a button). It can also determine which player has which gamepad when they're used to make assignments in button config.