I'm suggesting a config option to allow players to separate the Pixelmon UI from the regular inventory and instead press a different button (e.g. 'p') to open the pixelmon UI.
I guess another solution would be to fix your inventory controls to not interfere with other mods, or add compatibility to those mods, but I feel this would be a much easier option.
Hopefully you accept my suggestion, as I currently find playing with the pixelmon mod to be absolutely infuriating.