I've installed Command Start and another brand that I cant think of on trucks with manual transmissions and on my wife's T-Bird SuperCoupe.
The T-Bird had a neutral switch on the transmission so that was easy. Besides being in neutral, the park brake also had to be on. The starter wont "overpower" a properly functioning park brake even if it did try to start in gear.

The one kit I installed on a truck had sensors that went on the shifter, under the boot. Unless it was in neutral the sensors didnt line up so it wouldn't start. The park brake also had to be on.

The Command Start kit I have in my truck has to be armed before it will work. By arming it you are aware that the remote start will work next time so you do it properly. It has to see the proper arming sequence or the remote starter wont work. With the engine running you set the park brake (the remote starter has to see the signal from the park brake switch) , press button #1 on the remote which keeps the engine running and turns on the park lights. Exit the truck. With the truck running you're not going to get out with it in gear....I sure hope. Once out you close the door and the remote starter sees the dome light go off. Press button #1 and then #2 on the remote. That shuts off the engine and arms the remote starter.
The sequence sounds like a bit of a nuisance but it really isnt a problem and it works well.