You took a car with aftermarket parts used to align the car and were surprised that a mechanic trained on factory equipment did not know how to adjust it using the aftermarket parts located under the hood when a typical alignment is done only under the car. You then called a shop that routinely handles cars with aftermarket suspensions and was then told that it was not a problem. Right? Coupons don't always save money.

In a dealership, it will always be hit or miss with getting a knowlegeable mechanic. You may have just gotten a mechanic who is inexperienced. If you see a car in the employee parking lot with lots of aftermarket equipment and sidework done, ask around to see who's car it is, request that person, and be willing to wait for his availability. Think of it like a haircut place. Not much skill required for the basics, but the good ones know what they are doing and work based on appointments. My youngest brother works at a dealership and has enough work by appointments and requests that he is no longer assigned walk-ins.

I'm not sure why someone would take off your door panel at all. If any work was performed, you are legally entitled to receive an estimate beforehand. As stated before, no one wants to do more work than they have to. The window is typically rolled down while in the shop or on a lift when the keys are in the car to prevent them from being locked inside. Confront the shop manager in a nice tone and he may ask the mechanic if he noticed something wrong with the window and removed the door panel without permission in a good faith effort to diagnose the problem for free.