I encountered some weird issues like using L3 to crouch triggering Dead Eye when the game detected mouse. And doing L3 + R3 to trigger Eagle eye making the camera look back when mouse is detected.
What I did for the Dead Eye was setting a chord so that when I use the input that actives mouse it turns L3 turn into Ctrl, so I can toggle crouch without issue. I have mouse gyro activated on a right pad touch, so I set the chord to right pad touch. If it were left trigger pull I would set it to left trigger pull.
And for eagle eye I simply bound middle mouse click instead of using L3+R3 to not have issues with mouse input is detected.
I played the game with a regular controller without any mouse input to get a feel for the game before moving onto mixing mouse inputs with gamepad, and I don't think I've encountered any other weird issues since aside from the usual icon flicker. But, if there are other oddities that come with mixing inputs in this I'd love to know.
Also, mouse stuttered in this game with a regular mouse too until I toggled on the slider for mouse smoothing.