I just ordered a bike from BikesDirect and researched online bikes very thoroughly. One thing I came across often that in case of warranty they send out the new part and it seems occasionally re-imburse the owner for LBS install cost. Wouldn't apply to me since I can do all work myself, but good to know that paying the added markup for LBS is not worth it in all cases.
I understand the LBS you took it to since you didn't buy it there. But I can take my honda to any honda dealer for warranty work and don't get stiffed for labor. Especially since labor is the largest cost most of the time.
But another point that seems a problem with LBS is, they should have told you upfront about the cost. Especially for warranty work you are under the assumption it is covered unless told otherwise. Seems sneaky to me.