Having worked at both a dealership and an independent repair shop, I'll chime in from the technician end.
One thing to remember is that while it's great to establish a relationship with a service writer/manager, all that person is ultimately responsible for is talking about your car. I would suggest when you talk with the up-front folks to ask if there's a technician there known for having a super clean car or for doing top shelf work (disclaimer, they don't always go hand in hand). See if you can meet them and build a relationship with them - show them your car, shoot the breeze and talk about what they do/have/use etc. Then, instead of the PITA "nut job", you're an enthusiast face with a really well cared for car. And, you'll be actually conversing with the person responsible for not wrecking your car.
So often, it seems technicians just don't know what clean is or how cars get/stay there. I've worked with many guys at the dealerships that were in no way, shape, or form car guys. It was just a job that paid. That kind of person will put no mental energy into thinking about what happens when you take a fender cover off that winter-road-filth crusted fender, fold it up, and later drag it onto the fender of the 'Geek level paint.
I would say I use fender covers (in cloth form; I hate the foam backed padded ones for grit reasons) about 2% of the time - the rest of the time I focus on approaching repairs so I'm just not making contact with paint.
I've got a coworker now that tries to care about cleaning cars, but still just doesn't get how sensitive clear is. Every time he washes the loaners, he's after them with a water blade first before finishing it with the crummy terry towels our uniform company provides. He just doesn't know any better (or see the difference).