So... first off, do you plan on having over an inch of standing water in the vehicle? A key's length is over an inch, there should never be that much water in the vehicle. As I said before, if you're in THAT deep of water, electronics are going to be only half the problems your running into.
The space above the connector is possibly for other junction connectors related to higher trim models. You have an SR5 which would not have as many modules and needs as say a Limited with RAS. Once again I will point out that the harness runs along the floor and can be a conduit for fluid as it is in ALL modern vehicles; of which can short out any number of modules if it gets into the junction block and/or common power sources.
Also, why is only your driver's side floorpan so badly rusted, are you purposefully dumping salt on it or something? I've seen what road salt does to vehicles and you should be seeing the same damage spread across the passenger side as well with the tunnel being fairly okay as the drivetrain takes the abuse of that.
Finally I am glad everything worked out for you in the end. Next time I would recommend you disconnect the battery before doing ANY washing of the vehicle interior and then letting it dry out properly before reassembly. It doesn't matter if its a 4Runner with a "low connector," Mercedes-Benz S Class, or a Dodge Neon; you're forcing water where its not supposed in a modern computer controlled vehicle and you're upset it has issues. That's unrealistic thinking, modern vehicles come with modern problems, dielectric grease won't stand up much against a pressure washer by the way.