Running Arma 3 Ports OS X version under 10.11 El Capitan (same behaviour seen in 10.9.5 Mavericks), when you have a secondary screen connected, the game things it is the main screen for all purposes except actual display, apparently. Resolution settings are restricted to maximum of 2nd screen (1680px in my case), and mouse input in fullscreen mode in the menus (main menu, map menus) does not work (only keyboard).

Setting output to Windowed allows normal mouse input, but resolution is still tied to 2nd screen maximum.
Although Windowed output has problems with GFX card not going into full power mode, resulting in low FPS.

Actually physically disconnecting the 2nd screen cable allows to change resolution to normal for the main screen (4K in my case).

Still, graphics settings are limited to Textures:Low and mostly High on Details and Terrain maximums, even though the GFX card has plenty of power to run most on Ultra.

Seems to be a problem with the eON wrapper not dealing correctly with multiple screen setups.