Most BM Dealers have set menus for servicing - best to check yours dealers website. Some will give you a small discount if you bought the bike from them. Any extras outside of the routine schedule will be more (if you know what i mean etc.....)
Most seem to be pretty fair on the unexpected IMO
I was quoted 100-150 pounds for the 6k service. However I changed the oil, filter and brake pads myself beforehand and the final bill was just under £75.
EBC would set you back a maximum of £60 for the whole set.
The only possible warranty contention I can see would be if you had to claim for brake disc wear.
Seeing as the BMW rear pads wear so fast (mine lasted 4k miles) I think the savings in brake pads will offset any potential disc costs I may incur in the future.