I don't have the board you're looking at and haven't played with the other firmwares, but EasyAVR really is easy. I also use Linux so am not much help with flashing in windows if those were the programs you were asking about...
Whichever firmware you chose the layout will be stored on the board but you can save the settings to tweak and rebuild later.
I doubt any of the programs have a dark mode but they may use your system's colours - you'll have to give them a try.