You know, I'd seen that little connector next to the air intake, and wondered just that. It might just be for a siren/horn? There are even holes on the wheel well to mount something....An Alarm horn? Hmmmmmm....
Well, I figure, than my remote panic switch can activate the horn and lights, and the computer knows when the doors are open when the doors haven't been unlocked with the remote, so it's just a programming change that would enable it to link the two functions.
I'd guess that if someone wants the alarm added, Toyota doesn't want to go installing a lot of hardware, other than the glass breakage sensor, (probably an easy addition), and a siren, although, maybe it just uses the horn, like so many other cars do.
They'd probably not want to make it a simple connector change, as people would figure it out, so they make it a setting in the computer. But who knows....
Anyway, you have a manual and I don't, and you sound like you know much more than I do.
BTW, I haven't found any Chilton or Haynes manuals yet. I take it you bought the Toyota manual?
Thanks.