NO, it sounds stupid, but i have heard Toyota doing this to try to single out aftermarket stuff mainly to find something else to blame other than their stuff.
I have read this same scenario on forums over the years, someone having an odd-ball issue and Toyota tells the owner to remove anything and everything aftermarket so they can count those things out as part of the issue. It isnt hard if you dont have anything done but it really sucks if you have all sorts of goodies like yourself.

Now, i have worked at a stereo shop for years back when i was younger, and kept up with my skills on my own stuff over the years. I have seen some hodge-podge BS come in the shops and wonder how people have not burned their vehicles to the ground over and over. A friend of mine owns a big stereo shop in town and i occasionally go in to grab something and almost every day hes fixing someone elses shoddy work and laughing as he pulls out rats nests from under the dash and amplifier wire run outside the A-pillar and thru the door jamb. Not saying your stuff is that caliber but Toyota is likely just wanting to try to rule out anything that you added but it would seem extremely EXTREMELY unlikely that aftermarket headlights and interior lights would mess with the passenger seat airbag system.

There is a pressure sensor under the seat, and its own wiring system that i believe goes to a box in the passengers floorboard. I would think the pressure sensor, plug under the seat, wiring that runs down the passengers floorboard, or that box in the kick panel would be a much more likely source of the problem.

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