I think you'll need to use R3 to change weapon modes in that case too (but that's an ok layout I think, it is also an occasional button).
The other solution is to change Settings > Input > Hotkeys > 'Hotkey Enable' to eg. R3 instead (then you can turn select back to it's normal assignment).
The colours were pushed hard in part to help things still work on poorer GBA screens, but I still prefer them bright and unfiltered, and will be leaving them that way for other ports!
Thanks!