Really a personal choice... depends on how good you are with the tech working on your car. I would def. disable the roof module till at least after they have done service. Then i'd enable it, and blow their socks off
As for the flasher. If you installed it with the car off, there will not be a "bulb out" error message stored. So at most like etyu said, you may need to explain to them that its a custom job, and the 3rd brake light is operating as it should. If you don't, they may start digging in there.
I am also going in for service on Monday (same as you). I am going to disable both the Kleyman 3BFM & the Roof module till after they are done working on the car. Then i'll give them a show.
My car's computer is however filled with tons of bulb out errors from working on the module, and all the led conversions, foglight HID conversion... so on. But i know my tech, so at most he just brings it to my attention as he did last time on my CLK. (had somewhere near 100 bulb out warnings... was testing out resistors/leds/new bulbs/HIDs on the CLK
)