Aside from that, consistency and themability are not at all mutually exclusive. Back in the early days of OS X, theming by hacking system resource files (or patching them in memory via haxies[0]) was quite popular and for the most part, worked very well — generally, the only apps that didn’t play nice with themes were those sitting in the uncanny valley between native and custom, using bits of both, which tended to not be the highest quality applications anyway. This was way before Apple started pushing devs to parameterize their apps, too, and so similar theming capabilities today would work even better since themes can just tweak the parameterized fonts, colors, etc as needed to maintain coherence and usablity.
The real problem with GNOME/GTK is simply that it wasn’t designed with user customization in mind even as a remote possibility. A UI framework that did keep these things in mind combined with a strong dev culture of parametrization would make for a desktop that’s both customizable and consistent.