Ok, I think I came up with a reasonable answer for Fouqes.
It seems that those who have an aftermarket remote start, can override the kill switch by placing the key in the ignition, right? If not, brake, gear shift even opening the hood, will kill the engine. Safety precaution, right?
The OEM remote start with the Smart Key, kills the engine when the door is opened right? So no key to put into the ignition to override. No way to override. The question is why?
The problem may be, that the vehicle can and does sense the smart key from a distance. What, 8-10 feet maybe? Whatever the distance, it may be enough so that the vehicle "thinks" the key is in or nearby the vehicle. But it is not really in the car. So you can't use the smart key like a real key to override the kill switch. With a smart key, somebody can get in the truck and drive away unless you use some other action to kill the engine, like opening a door.
To overkill this, let's say you keep your smart key on a hook just inside your walk through garage door and your vehicle is parked just inside your garage. The distance can be only a few feet. You open your garage door (for exhaust), remote start to warm up the truck. Close the walk through door and wait.
Somebody walks up your driveway, see's a running car, tries to get in to steal it. Aftermarket, soon as the brake or gear shift is touched. Car stops.
Smart key, open door, car stops. Theft is defeated. Does this make sense?
I have thought the same, and my concerns were the same (damn good ideas, btw!). But here is the pickle.
1) Proximity of the key is a very sensitive question. Matter of fact, if you stand a few steps away from the vehicle, it does not sense your presence, thus does not allow for opening a door.
2) With a smart key, you still have the "takeover" step. Same as putting your key in the ignition. You get in the car with your key, depress the pedal, system checks for the key. If signal is recognized, then it goes through a takeover phase; else it shuts motor down.
3) If your running vehicle leaves the proximity of the key (someone drives off while you're chatting your hot neighbor), vehicle shuts down.
the # 3 we tested in my lady's and my client's cars; we haven't tested it in the limiteds, but I refuse to think that Toyota is less intelligent (or secure) than Nissan.
I understand what you're doing, throwing ideas out there is great, but so far every single concern that i've seen, read or heard falls into one of the following :
1) Person (such as yourself) is doing the only logical thing, try to come up with possible reasons - no ability to do a research, due to no test subjects.
2) Installer has no idea how to approach the install, and is lying to the customer to avoid having to deal with a difficult project.
3) A client of the above installer takes things as the ultimate truth, and shares it with others
4) Person just doesn't really want to make any research, and just tells people what his/her uneducated guess is, claiming it to be true.
Please, understand, I am not attacking anyone, just explaining what I've been encountering in a few years of working with shops / building cars.
Again, I do agree with you that it could be an area of concern, but the installers i've dealt with to this day have shown me that our concerns don't really stand the ground.
now, I would not say that it is impossible for an installer to botch up an install.. And, perhaps, the reason why toyota is doing this is to prevent extra questions and extra liability.
). I also wonder why it is so, and, just like yourself, have only speculation on the topic. I was not trying to argue with your points, I was just throwing out there the facts that I know to be true. I mean, isn't this the way how many discoveries are made? 
