Full height window is not full height El Capitan
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.