First of all, as a Steam Controller user, I was ecstatic to see this option and its description in Valhalla's menu. Really appreciate the option to flip the joysticks for specific uses as well. Didn't think Ubisoft would do something like this the third time around, and I'm absolutely glad that they did - especially since they love to change joystick deadzones and response curves for things like aiming, which makes using joystick emulation quite the pain. So, for that, I salute you. Maybe someone over there bought a Steam Controller on that last sale, huh?
But, it is currently broken, even if it is kind of usable. Not only does switching input modes make the game freeze for a moment, menus are completely non-navigable through mixed inputs. I have to resort to using my keyboard and mouse because of this, just for navigating the menus.
A simple fix for this would be to map the mouse to the joystick cursor or vice-versa, or even mapping mouse movement to scrolling - DOOM 2016 does something like the latter in its automap, although the mouse sensitivity setting sadly doesn't apply for that implementation.
Not only that, but mouse sensitivity in this mode seems to be far higher than when just using regular KBM, which is precisely the opposite of what you'd want for say, a Steam Controller, or even a regular mouse with high DPI - you'd want very low in-game sensitivity and high sensitivity on the controller/mouse, for smoother aiming and better precision.
Given the game's current overall glitchiness, I get that this is a niche use-case that shouldn't be high priority - but it also shouldn't require that much legwork to fix, and it would be an absolute godsend: "How you play can be just as important as what you play".