I have a 5 speed GT with remote start. The system I have is made by CompuStar. You can check them out at www.compustar.org.
The system I have is a combination of alarm and remote start. There is no need to worry about starting the car while it's in gear becauuse there when you want to remote start it, before you leave the car, you have to set what is called reservation mode. In my car what I do when I park is put it in neutral then pull up the ebrake. The doors then unlock and you hear a tick. When you hear that tick, you take your key out, close the door and you're good to go. If you don't set reservation mode, it just won't remote start. So there is never a chance of you remote starting in gear and hurting someone or fuckin up your car.