Sounds like the DTC was stored mainly on the ABS side of the vehicle, which is why you needed a scanner that could speak to the ABS module (it lives on an isolated network from the OBDII system and only communicates through the ECM.) Though I don't recall that setting an MIL usually (not unlikely though, its just been a while since I had a stop lamp circuit DTC come in the shop.)
Most dealerships charge a flat diagnostic fee to pull codes and determine the issue within about .8hrs of labor (if its more than that to do additional testing, the technicians will talk to the service writer to try and sell additional time), usually we end up just pulling the codes, P&A the part, and quote labor and such. But other times we (royal we including all technicians) actually have to get off our lazy butts and do diagnostic work.