Platform Dependent Project Settings.

You can't do that, at least not officially. You could swap out the InputManager.asset file every time you make a build, but it wouldn't help if you want to support more than one gamepad type.

The normal way of handling cross-platform input is by either creating your own input manager or buying an input manager system from the Asset Store. Most input managers that wrap UnityEngine.Input will create an exhaustive list of Axes in the input manager, one for each possible axis on every joystick id. You poll the Axes in the input manager for all connected joysticks to get the axis values. For buttons, you poll Input.GetKey using KeyCodes for all buttons on all possible joysticks. Then, to make things cross-platform, you need a system that maps from a pre-defined controller definition that you've created (for each supported platform) to a standardized layout. Then your code can just reference the standardized layout. It can get very involved and be very time consuming to create an input manager like this, especially if you want to support more than a few controllers. There are some good input managers on the Asset Store that can do this including my own Rewired, which does this and a whole lot more.