When you call emacsclient like this: emacsclient -c -F "((fullscreen . maximized))"
the maximization ignores the size hints and some residual area could be left behind, looking like a phantom modeline below the real one. This doesn't happen when you manually or programatically maximize emacs after launch. Extra space could be reserved at the east and south edges, of course, because of the multiple-of-char-size restriction, but this extra space is correctly painted with the background color. It seems to me like some issue with the order of the initialization sequence. Nevertheless, I believe this is mostly irrelevant for 24.4 as the multiple-of-char-size restriction would be no more binding.