Thanks Max. I see what you mean.
I looked into this further and it looks like this mainly occurs with the "tall" human tiles and some of the goblin tiles. This is definitely more apparent in human libraries or libraries with more humans. Specifically most of the robed humans and a few of robed scholarly goblin tiles.
The dwarves are shorter than 12 pixels (or shorter than 24 pixels if one is using the 24p settings), so there is a definite separation for that set. While the elves do reach a height of 12 pixels like the humans, their hair color separates the two (especially since the majority of the time they don't wear hats/helms and when they do they are made of wood or foliage).
I did try your suggestion, but that made the the human tiles look short when height was part of the focus for them. But, you are right about the stacking. So, after thinking on it for a bit, I tried something a little different.
For the humans I differentiated the top color of the tile (rather than the bottom) to keep their height (even when stacked) . . .
. . . and for the goblins I made the robes shorter in addition to changing the top color on the taller hats.
This keeps the height differences (which I like) and also inadvertently fixes that nagging sensation I got when I looked at the human keffiyehs.
I updated the download and the snapshot in the OP,
but I did NOT update the screencap you linked to (yet). In the meantime, here are two screenshots with the fix in place (one is a manually edited version of the screencap you linked to for reference):
Thanks again Max.
February 4th, 2017
** Various tweaks to most robed professions for Human and Goblin civs to prevent odd stacking.edit: I've since edited the screencap Max linked to. For clarity, this is what he saw: