I've just discovered the answer to my second question regarding Macintosh modifier keys. It appears that KDE's keyboard tool for switching between multiple languages is to blame. KDE has no Macintosh keyboard layout, and its forcing the layout to "generic 104" any time I switch languages, despite the fact that I have XF86Config set to use a Mac keyboard, and despite the fact I tell KDE to use Mac keyboard modifiers. If anyone can think of a solution to this I'd be grateful.
