Full height window is not full height El Capitan

Solution 1:

The gap at the bottom of the window happens when your Dock is placed at the bottom of the screen and hidden. If it is visible, there is no gap, and if the Dock is placed to the side of the screen, the gap appears on that side when it is hidden.

I'm not aware of any way to disable this behavior, but it has been present in OS X for some time.

If you are looking for maximum window size, you could try Full Screen mode, which fills the entire screen with the contents of the window, and even hides the menu and title bars.

Solution 2:

Apple designs the screens to leave a gap between the top window and the menu bar (especially noticeable with a dark menu bar and a bright background image) and also maintains a gap between the physical bottom of the screen and the window.

If I were to guess, it's to preserve shadows and "depth" of the interface and they made a conscious decision to implement windowing this way.

You might have to file some bug reports and gather use cases for how this is bad to get them to reverse this decision. It's hard to unsee once you notice it, but I don't think it's just a bug in their code.