I would think that any "bypass kit" would perform a check as basic as reading the transmission state; whether in neutral or not?!??
For liability reasons companies refuse to put remote starting capability in manual shift vehicles. Yes, in theory you can maybe wake up the computer and maybe read the transmission's Neutral Position Sensor state, but what if the sensor or the connection to it becomes compromised? What if the eBrake is less than 100% reliable; what is it's backup? In my prior car, had the connection to the sensor break loose and have had the eBrake lever snap-loose (minutes later) because I unwittingly set it on the edge of a tooth. Due to worn adjusters it also wouldn't hold on REALLY steep grades and, get this, the engine wouldn't either. So in those circumstances I just had to park it somewhere else.
One concern mentioned in the thread below was, the possible security drawbacks of having the car (or rather, a program running on it,) always connected to a public network.
http://www.fiestastforum.com/forum/threads/12115-Ford-to-expand-Sync-3-capabilities-CES-2017