The 'hide window controls' option is pretty obscure these days, since the Acrobat Family uses SDI it doesn't do anything useful, quite the opposite - it removes the scroll bars, status bar and the left side panel. You can bring the panel back with F4 or right-clicking on the canvas and selecting "Show navigation pane buttons", but the scroll bars can't be turned on by the user, and they're pretty important! I wouldn't advise setting that option anymore, it will simply annoy people for no reason.
The color change is just a by-product of how the UI is constructed. Don't expect it to last.