I don't know the reason for the typically high tire prices at BMW dealerships but I don't care about it becasue I don't buy tires there. Get em by mail and use a local cruiser/sport bike shop or a friend's place. Sometimes the local shop I use can match the mailorder price so tires can be bought there..
I buy BMW parts from my local dealer or one of te larger mailorder places, depending on what I need and where I am. Prices aren't always the cheapest but I can't claim to hve been gouged by anyone. I like the fact that it is easier to get parts for old BMWs than for relatively new J-brand bikes- that's got to be paid for somehow. Besides, I try to learn something from the shop guys when I visit a dealership..
I saw a guy on an GS remove both wheels (centerstand and a side case stuffed under the engine) in the parking lot of "A big dealer in the N/E" and carry them inside to have tires put on. When his tires were ready the service department loaned him a torque wrench to re-install his wheels.
I generally mail order parts from A&S in California. I signed up for their email updates and every so often they have a "gift" if you order a certain amount. If the gift is something I want I will order those types of things I use, filters, oil, etc. The value of the gift usually exceeds the cost of shipping, plus there is no sales tax if you are outside of CA which, unfortunately I am for the next few months.
My experience has been that there are two types of dealer parts operations. Those that stay "local" and do not staff up and try and capture the internet or regional markets, and those that do. The former charge more than MSRP in an attempt to increase profits. The latter offer a discount and depend on volume to make up the difference. I also think the former is a little shortsight particularly when you realize that BMW dealers are geographically sparse in may parts of the country.
BTW, the guy behind the counter can change the parts price while you are standing there. So if you are the guy who went down the road to save $200 on your new bike after you wore the sales staff down, guess what.