So if someone cloned your key fob, the starter relay would automatically disarm and allow the vehicle to be started.
Key cloning is easy to prevent. Leave your keys in a Faraday box instead of sitting out.
The more likely theft scenario is for the thief to break your window, reach in to unlock the door, hop in, program a new fob to your truck, press the start button and drive off. This wouldn't flash the parking lights, so hooking the hardwired transmitter to the parking lights would thwart this scenario.
It would work, yes - but it wouldn't be very secure.
I agree on the level of security, though. There is a pretty good chance a thief, who has just programmed a new fob and finds the truck doesn't start, will start mashing buttons on his new fob to see if the programming was successful. He will probably hit lock/unlock and flash the parking lights.
Another alternative to the parking lights is to put the hardwired transmitter on something less likely to be triggered by a thief, like the tailgate release. Then to remote start, you've got to pop your tailgate, and flop it back up before you drive off.
I don't know if there's a circuit EXCLUSIVELY activated during remote start that would do what you're looking to do.
There is, but it'll take a little bit of investigating to figure it out. There's likely a wire from the module that does the remote start that can be tapped. I need to see a wiring diagram. Wiring the hardwired transmitter to this wire would allow the vehicle to remote start, but not button start. To button start, you'd have to use the relay's fob. Or, to forego the relay's fob, you could use two hardwired transmitters, one on the wire from the remote start module and one on a hidden switch or something like your brights that you can actuate when you're at the truck. The hardwired transmitters are cheap ($30), so having more than one isn't a big deal.
As an aside, keeping remote start is a risk, too. If the truck can remote start, and the thief has programmed a new fob, he can remote start it with the new fob, press the start button and drive off.