I don't think it would be all that confusing... but for me it doesn't really matter. I've gotten used to simply sticking with whichever seat in each pit that gives me the best view for both flying and weapons use (front seat in the Comanche, back seat in the Longbow; haven't started flying the additional US helos nor any of the Russian ones yet). I have macros that select both MFD assignments with single button pushes, so relying on ESC to toggle between two setups isn't all that important.
The annoying thing (but I guess realistic) would be taking the time to set up both seats before takeoff, or at least before engagement, so that you could even take advantage of this feature.
I like Re-Ordained suggestion above: Have an eech.ini setting that designates if selections made by the user in one seat it is mirrored in the other seat or not.
Keep in mind that right now MFD settings are already NOT mirrored between seats, so consideration should go into whether or not folks setting this option to always mirror settings would also mirror MFD selection. Maybe this would be a secondary setting in eech.ini if the first option is enabled?
I'd warn against adding so many options to the eech.ini from an accessibility standpoint, but there's already plenty packed in there anyway. Might as well go all out!
Side question since this thread is about avionics, after all: would it be possible to add specific keystrokes to select specific weapons? Right now Alt+Backspace can select the Cannon with a single keystroke, but all other weapons have to be cycled through. I'd love to be able to switch directly to Stingers if enemy helos pop over a ridge while I'm trying to shoot tanks. 9/10 times I get shot down specifically because I'm trying to cycle to a specific weapon and overshoot because it's a cycle and not a direct selection.
Do real attack helicopter gunners actually push a single button multiple times to cycle through all of their available weapons and this is just replicated in the sim, or is this a situation where the real thing has a different button for each weapon and the sim is taking liberties due to limited keystroke combinations being available?