I think you're making this a little bit more complicated than necessary. Those gadgets are cool but that would probably require more support by the devs than a simple keybinds and considering how niche this stuff is... I think the latter is a more probable option.
Those two axis you mentioned would be modified together anyway since we'd want the speed modifier to be the same no matter the direction. Alternatively one could make it into a separate variable included in speed calculations - this way you can keep the direct input value provided by the controller (whether it's a gamepad or a keyboard) and have one more piece that can sit unchanged when playing with analog controls.
Mouse scroll was an example since that's how it worked in Splinter Cell back in the day (it's also how Star Citizen does it today). You could just as well use any other key to increase/decrease the this muliplier (or make it mouse scroll + modifier key).
Overall, I do agree that more flexibility in input mapping would be a good thing. Can't go wrong with giving people more choice.