Firmware should be done in C/C++ code (not Arduino code), fast, small code and near industry standard.
Depending on your electronics skills, bluetooth "module" could be a HC one, without need to have a PCB for Arduino.
I can make the communication of the device binary, that has less overhead, being faster, needing less computing time, but will not allow easy connection from a ASCII software.
The set command can be [7h][R][G][B][n][a]. That's 6 bytes for the command, add one byte for other light. The first byte is the command, R, G, and B are the bytes for intensity, n the number of lights that will be set, a will be the light that will be set. Compared to the worst case eg R255G255B255P15 that's 15 bytes.
The application will be developed on Windows, .Net, so It should run on most platforms, even on Linux, maybe with small modifications.
You will be employing an professional with vastly experience.
Ps: This price does not include the "Stage 2". Also it only includes software work (if you need I can make schematics, and PCB so you don't depends on Arduino board at other price).
ATMega168 is so much for this project, from the little resume will said, a cents of dollar microcontroller will do the job.
Using Arduino board for development can be good depending on your skills, but for production scale I can help you further.