We think it is that the cursor is locked to an input field, and therefore disabling keybinds for Mac.
If this is the issue, it might be caused with what type of bindings you use. Just browsing through the .dso source, I notice that most of the common keybinds (e.g. moveforward, brick controls) use moveMap.bind(...). However, some more important keybinds such as toggleConsole, toggleFullScreen, etc use GlobalActionMap.bind(...)
For example:
GlobalActionMap.bind(keyboard, "tilde", toggleConsole);
GlobalActionMap.bindCmd(keyboard, "alt enter", "", "togFullScreen();");
GlobalActionMap.bindCmd(keyboard, "F1", "", "contextHelp();");
moveMap is just declared in the .dso with:
new ActionMap(moveMap){};
However, GlobalActionMap isn't created anywhere in the .dso source, meaning that it is more than likely created in the engine, possibly giving it special properties.
Somewhat speculative, but worth investigating in my opinion.