The Cube
I always use some silicone lube on the caliper piston where the dust boot rides before I screw them in. It might be a good idea to open the bleeder valve before you screw them in too. The shop that told you that you could seriously mess up the brakes was probably talking about damaging the rear calipers when you reset the pistons. The square cut seal that keeps the brake fluid from leaking by the piston can be damaged when you screw them back. The good news here is that if you do what you can to minimize the pressure on those seals (open the bleeder valve), you'll pop the same number of seals that the shop will in the long run. I doubt that you'll have a problem here, but it is always a possibility. I'd feel pretty confident with a fairly new car that the job would go smoothly.
edit-the guy who told Badger that the calipers could make the master go bad is FOS. Call the dealer and see what they're charging for the same job. $111 for a system flush seems ridiculous unless there is some ungodly expensive special fluid required.