The thieves electronically rekeyed or added another fob to the trucks' ECU. You noticed the thieves crawled through the window instead of opening the door - that would've triggered the car alarm and a 5 minute lock-out unless you cancel the alarm with an existing fob. Adding a tremble and/or glass breakage switch may have avoided this thief. A smart thief would run away as soon as an alarm is triggered. If they find that car, they can see who's credentials was used to add the fob. We leave electronic fingerprints everywhere, that's why your not suppose to share your electronic access credentials. I had a cheap department manager try to make me give up and share my credentials with the rest of our shop after I got back from training. I told him to put that in writing and I also need an official letter drafted by our company lawyers, that I will not be held accountable if someone reprograms a system and it results in injury or death of someone. I never got that letter. The second thief shouldn't have happened to begin with; IMHO. Relay spoofing a fob is well known and could've easily been avoided by placing the fob in a metal box or fariday bag. Live and learn......
Just got my promised second key, programmed at the dealer. Don't have to tell you, unless pressed into service, that fob will never leave my faraday box (except to pull out and check for battery-good, every month or so)
you can turn-off that secondary fob, once you make sure it works and the back-up manual key works. option #2 on the link. How to Disable Your Toyota's Smart Key System (3 Easy Methods)