Over tightened wheel nuts are a complete nightmare. I got a flat in the middle of nowhere at night and found that the idiot who had fitted my new tyres had done this. I couldn't get the wheel off with an extra long wrench I was jumping on. Wheel fitting places fit into the equation a few rungs below car dealers.
Les Schwab has provided consistently excellent service to me over the years. I can't speak for other tire places but of the four Les Schwabs I have done business with I have never had a single problem.
From my personal experience dealers are much worse than tire shops but I'm not going to claim that's true in general.
Anytime I've had to bring my car to a shop, for any reason. I've run around each bolt, loosened, and properly torqued. Things like an inspection, will take at least a wheel off, and dealing with warped rotors, blows.
This is a really good practice but not everyone has the experience tools, time and space to do this. Not to toot my own horn (hah) but I am capable of performing any repair that has come up for my car but I still pay a mechanic most of the time because after moving to a city I don't have the space for my tools or a place to work on the car.
It's unfortunate that the shop that carries the manufacturers name is not a trustworthy place to have the work done, even with their exorbitant premium on labor.