Question, have you had suspicious people in your area loitering in a car and/or with large bags? Typically what I have heard is that they're using a powerful antennae to pick up the RIFD signal from the street when you enter/leave a vehicle and cloning the Immobilizer signal that way. Only Toyota Smart Keys use a rolling key code as of right now, so it's a very simple thing to defeat that way.
I'm not saying someone at the dealership couldn't have done it, but holding the vehicle all day for a service is actually not as uncommon as you might think. At our dealership we'd much rather the customer leave it for the day so we can better dispatch priority work vs. rushing everything out the door (more likely to cause mistakes, errors, ect.) But it is possible someone could have copied the key and/or obtained the key code.
Thieves have quickly adapted to changing times, so even the most modern security measures are only an inconvenience to serious/organized car thieves. Lo Jack is a good system, we install it at the dealership; but from what I have seen and read up on their design, they too can be defeated and possibly jammed given the right equipment (though this is more rare from what I read if not proven; more theoretical.)
Best of luck in recovering it, I find it odd that they ditched your gear on your neighbor's yard; that seems weird to me at least.