Yes, Apple takes excellent care of their BTO customers (and it really doesn't take that long unless you are purchasing something unique or new to the market).
Although avoiding taxes is always ideal, it's usually safer to buy from them (they will rarely hesitate to accept a returned good, I can't say the same for some of the others).
Many Mac users do talk highly of Mac Warehouse / Mac Zone, but I would watch out for any others unless they are authorized Apple resellers.