Leonhard,
Sorry for the slow response to this.
In the Table 9, there are default bits shown below each bit name. So for example EN_AGC = 1 by default and EN_SYNC = 0 by default.
When using the default mode the EN_SYNC bit is forced to '1'. GAIN_SEL = 101, MODE_CTRL = 01, SPEED_CTRL=01. The default mode is controlled with the AMODE pin.
It is not possible to permanently save commands. The registers will be set to default value after power off - power on cycle.
Setting DME pin to '1' starts up the boost and therefore I would recommend you to use this with the boost components.
For the controller side I cannot give any recommendations.
If you are looking for more complex fading/LED control programmability you might want to take a look on the LP5523.
Hope these answers at least some of your questions.
Regards,
Sami