Yeah, the routing was difficult. I did it with kicad, it took me i think about 5 attempts.
Regarding your questions:
1) yes, correct. White soldermask is just a tiny bit more expensive than green at http://www.multipcb.de/. I can really recommend them by the way.
2) I don't get that, sorry. I have all module connected in one row, therefore there is one input and one output on each PCB. It connects the DIN and the I2C bus (for the LEDs)
3) No, 0.125W would not be enough. Each array drives 16 LEDs. Unfortunaltely, the PC!9635 requires resistors, I would have liked a part with constant current regulator, but I did not find one that suited me.
4) Yes, they determine the I2C address of the driver chip, which has to be different for each chip. There are three on each PCB, one for each color.
5) Yes, more or less. one signal layer, one ground layer, a mixed power/additional PWM layer and one layer only for PWM (of the LEDs)