At my previous agency we removed the lightbars and other lights and reused, saved for parts if current model, or sold at auction. Radios and antennas were removed, ordered new harnesses, and installed in new units. If out of date then sold back to radio dealer to upgrade. Consoles were usually wore out and we left them. Lighting and siren controls were reused if in good shape. If not then saved for spare parts. Siren speaker was usually reused. Camera system and radar systems reused. Cages went to scrap metal. Wiring cut as items were removed. Order new harnesses each time. Harnesses are cheap. Paying for labor to remove wires is expensive. Decals were removed. Antenna and lightbar holes plugged. We didn't have ballistic panels. Spotlights stayed unless we needed for parts for another unit. At my current agency it is a lease.
There was no dealer work done. We did not pay to reprogram the unit or remove factory parts. You do what is cheapest for the government. It doesn't make sense to pay big hourly labor at a dealer on a vehicle you are getting rid of. Goes to auction as is. Their is no de-program, detune, or downgrade the ECM. The dealer may check for recalls or bulletins and re-program the ECM based upon that, but that is to correct an issue; not to "detune" a vehicle for sale to the general public.
Did you ask if they re-programed the ECM? If they did re-program did you ask why? Was there any other outstanding service bulletin or recall? They would have no reason to flash the ECM for the toe link recall and the tech/dealership would not be making money by messing around with the ECM. Dealers are in the business of making money and generally don't perform any more work than what they are getting paid for. If you are not sure you can read the ignition count to see how many key cycles you have. If you have a very low number of key cycles then your ECM has recently been flashed.
Have they reviewed camera footage of the dealership? Every dealership I know has cameras. Did PD review them for activity? Also are you certain you had ballistic panels? How do you know they removed them? And the glass is the same between Explorers and PIU. There is no ballistic glass.