With a GTK3 build I start Emacs with the following initial file
contents:

(customize-set-variable
  'default-frame-alist
  '((cursor-color . "red3")
    (width . 80)
    (height . 32)))

Here this results in a frame that is 36 lines high, has a root window of
31 lines and a minibuffer window of 1 line.  The remaining four lines at
the bottom of the frame are (more or less) empty.

I traced this behavior back to

Fix redisplay performance problems with some fonts
* src/font.c (font_list_entities): Revert part of the changes
introduced on Apr 2, 2014 to fix bug#17125.  It turns out having
zero_vector in the font-cache is an important indication that
cannot be removed.  (Bug#21028)

Commit f3b24e90dc9fad355102e1fdf2828ca33d447a07 does not have the bug
while commit 58430f29968a5661caff630d20dbbe7c864fe08d has it, see the
attached screenshots.

Reverting 58430f29968a5661caff630d20dbbe7c864fe08d with current master
does _not_ fix the bug, so something else must be at play here too.

This is with stable Debian running xfce 4.12 and xfwm4.  I suppose that
various behaviors sketched in Bug#31745 might be related but I have no
idea how the font_list_entities fix could have affected frame creation
in the first place, so these are only wild speculations.  As mentioned
there as well, the bug is GTK3-only, GTK2/Lucid/Motif/None builds are
not affected.

martin