I think I'll try to explain this given that my father owns a Ford dealership, and I have experienced this "service" at my local Toyota dealership, as well.
1. Dealerships are required to purchase parts from the factory supplier at a certain price. I guarantee you, it will be 2-3X the price you will pay at your local auto parts chain store. In fact, when I was getting genuine OEM Ford factory parts for my Ford Mustang on-line, the prices were significantly less than what my father's parts department could get them...even if I had my father order them with his 30% discount. Aftermarket parts may be inferior quality, they may actually be identical to the OEM part (because they are a factory supplier), or they may be superior to OEM parts. Bottom line, avoid purchasing parts from your dealership unless absolutely necessary. Some dealerships will work with you if you choose to have them install non-OEM parts. They will typically not guarantee their work...the risk is yours.
2. That $90/day overnight charge is likely liability insurance should anything happen to your vehicle inside the shop or outside. Not every shop will tack on this charge.
3. Then there is the "labor cost scam". Example: You need a ball joint and tie rod end replacement. So you go to the local dealership. They look in their "magic book" that the says, "X" amount of labor to remove a wheel, "Y" amount of labor to remove and install a new control arm....What?...You just wanted a ball joint! Well, the factory does not supply the dealerships with ball joints. They want the dealership to buy the whole control arm assembly that includes the ball joint. Then, there is "Z" amount of labor to install a new tie rod end. Then, because of the new tie rod end and control arm assembly ($750), they tack on the labor for a new front end alignment. The next thing you know, you're looking at a $1500 bill. WTF! Here's the labor cost scam. They charge you labor to remove the wheel, then they charge you the labor to install this control arm...which includes the removal of the wheel. You've just got charged twice! If you want the tie rod end changed, then this also includes the time to remove the wheel. You've just got charged three times!
Since this is a true story, I'll tell you what happened. I had them go to Autozone (across the street from the dealership) and pick up a new ball joint ($65) had them remove and press it in. Then, after being raped for $450 to do the job. I drove over to the Autozone, picked up 2 new tie rod ends for a grand total of $20. Drove home, and in 30 minutes, I had installed them in my driveway. No alignment needed.
Rent, borrow, purchase tools. Get yourself a service manual for your vehicle. Get yourself a general mechanics instruction manual. Save yourself a #$%^ load of money. Trade-off being greasy hands, scuffed knuckles, more time than a professional to do the job, and lot of cursing.
