With an environment where a user has the application Menu on top of the screen as a global menu, if the setting "focus follows mouse" is active, then the menu becomes jarring to use. This happens for example if several applications are opened and the one in the background has its window a bit higher than the current active application - when the user wants to select an item of the menu of the current active application, and goes "up" with the mouse, the mouse will hover by the application behind and the menu changes (or disappears if that app has none), making its use impossible in this case. One cannot use this new menu "style" with applications higher than the current one, unless he always moves higher the current application window in relation to the others.
Well, it's in the nature of focus follows mouse that once you hover another window it will get focus.
There's the possibility to add a delay till the window gets focus. I suggest to use that and set it to a sensible value which works for you.