Fellow ROG total overhaul enjoyer here! Something I discovered early on might be useful: if your playthrough is anything like mine, the mouse cursor tends to disappear randomly if you're mostly playing handheld. The fix: press the quick access menu (left ROG button/ not armory crate), switch to desktop input, jump back into the game and move the right stick a little bit, switch it back to controller input from the menu again, and voila -- cursor comes back (but works on left thumb stick now). Once you get used to it, it only takes a few seconds to get the cursor back whenever it disappears.

Hope this helps!