Scroll bars don't fade out if you're using a mouse (as opposed to just a trackpad) or if you've set Mac OS Settings > Appearance > Show scroll bars to "Always".
I recommend changing the ⌘-` shortcut to ⌘-§, which is right above Tab on Mac keyboards (Preferences > Keyboard > Shortcuts > Keyboard > Move focus to next window).
Having both in the same area of the keyboard makes my brain happy.