Window spacing is actually in the works for Amethyst. It just has some issues because some windows just don't size exactly. Terminal windows, for example, only size in increments of cursor size, so you're almost always a bit smaller or a bit larger than you want, which makes the spacing in between windows look weird.

I noticed that with or without my spectacle patch.

I tend to prefer uneven gaps than no gaps though, considering how unpleasant overlapping drop shadows looks like.