[Freon]

Registered? Programmed? Even if replaced with the same model? That's really unusual.

It does sound like they had to do some troubleshooting to find out you had an amp and eq that were not properly relayed to turn off without the key in the ignition. I'm sure that was part of the labor charge, possibly a significant portion. Sure, physically swapping the battery shouldn't take more than 15 minutes.

I'm curious how you have your amp/eq wired to stay on more than 0 seconds but less than 61 after the key is removed. Generally people wire the "remote" turn on lead straight to an "ignition" source which should be immediate. How sure are you this is wired properly?