remote start

ive got a 96 manual car, and i have a remote start kit for it that im debating on installing, the thing is i need a kit that basically puts another key in the dash so it can read the microchip in the car so it can start without a key in the ignition,

but my question is will that make it able to start if it is broken into and the ignition cylender is removed, since there will be another key in there and have the micro chip signal there all the time?

this i know, im not worried about it being stolen after i remote start it, im worried about it being stolen because of the key chip being in the car (the key's on 96+ stangs control the fuel pump. ecu. etc.... so without the key (or more specifcally the chip inside the key) the car CANT run even if its hot wired,

but with the remote start system it puts a transponder and a key inside the dash so that when you tell the car to remote start it recognizes the key in the dash, now would that also be recognized if someone broke into the car and tried to hot wire it?