Thanks for asking. I like the idea.
Ultimately, it would not necessarily make it more confusing, just different than the current. If the objective is to add difficulty, it would achieve this due to the additional setup required to have all weapons and sensors configured, prior to encountering a threat. If the objective is to add realism, my opinion is it would only go half way, meaning the pilots tasks would be different based on a two seat arrangement (real), but then that realism is reduced when one virtual pilot has to think as if he is two different personalities (not real). More challenging, not necessarily more real. A matter of preference, I guess.
For me, what it boils down to is, what sensors would be available most immediately and in the best configuration? Quick execution. If I'm occupying the front seat heads down in the ORT with hellfire selected and co-pilot calls out a close immediate threat, if switching seats to fire cannon at the close threat is more easily available with a one button push (esc), than that's the way to go for me.
My take is, does it make sense to limit the current sensor and/or weapon to one seat at a time? Only if one requires an additional element of difficulty. Kinda like engine realism. If it's not too much more work to make it an optional feature (like engine realism), maybe you can add it as an option.
You may be exploring the future possibilities of what other developers will face if they attempt to pull off a two seat sim and offer the option of one or two players occupying that aircraft in a multiplayer environment.
Needless to say, I love your work.