Keep in mind that it's very dificult to use the same exposure for all the filters and adjust only the pannel brightnes.
I have an Atik 383 with a shooter that needs at least 2s of exposure to hide the shadow of the shooter, so i use about 2 seconds expusure with the brightness set to 90 (in a range 0-255) for Luminance, but for HA filter, with the brightness set to maximum, i have to rise the exposure. This will hapen with a DIY Flat Pannel or with a comercial one. It will be the same.
Yes the Arduino board will manage the brightness of the EL Pannel using PWM. The board will receive the value from Ekos (or another client).
A word of advice. It's very difficult to mantain a very low value of brightness of the EL Pannel without flickering (mine starts to flickering at below of a value of 50-60). There are diferent ways to connect the EL Pannel to arduino, some more elaborated then others, but you can start with something as simple as a Mosfet.
So, if you will do flats with a C11 and a CMOS, i have no doubt that you have to use very low values of brightness, or using something to lower the brightness without dimmering the EL Pannel (some sheets of paper, for example).