Depends on how much is involved in the change. Lots of dealers will charge you a minimum of one hour's time for any job, to include bringing the car in, connecting up the diagnostics, filling out the paperwork and etc. The additional time needed to perform a simple one-bit setting change such as Autolock should be only a few minutes, and covered within that charge - but I don't run a dealership, and they may differ.
Then there are things they are prohibited from doing, such as turning down the EGR settings. VAG-com (or VCDS as it's now known, to escape Volkswagen AG's trademark) can soon pay for itself.