I would say that the BCS and BrewTroller replace the PID functionality and provide a bunch of additional functionality.
As far as switches and pilot lights, it really depends on what you want to do with your setup and whether you want to build in manual overrides for the automation components. With my BrewTroller, I have it setup so that I can let it run the show or if it dies or is not cooperating, I can control manually. The exception is the control of the heating element, I only have manual on / manual off / automatic so if the BrewTroller wasn't working, I wouldn't have a way to operating in any type of PID mode. In theory this could be improved by replacing my override switch for the element with some type of PWM controller.