i'm not really sure how engine cutoffs work in modern car alarms, but i just a vision where you would need your empeg to start your car. probably needs hella custom wiring... but heres my idea.
using one of the unused connectors on the empeg, it could complete the ignition circuit only if its in the tray. basically, split the ignition wire so it goes to both the fuse panel and the empeg (w/ a fuse somewhere). put in a blown fuse for the ignition at the panel, so theres only one way for it to go... and walla. cant start your car w/o your empeg in there.
if you ever lose your empeg, just replace the fuse (the thief wouldnt know to do that), and be depressed while driving.