I'm pretty sure this a GTK+ issue where it hardcodes some bad defaults forcing themes or apps to fix with custom CSS like [this Issue](https://github.com/shimmerproject/Greybird/pull/248). I guess this is the same as [this Thunar bug](https://bugzilla.xfce.org/show_bug.cgi?id=16050) linked from a (possibly) related [Mousepad bug](https://bugzilla.xfce.org/show_bug.cgi?id=16048).
IMO, such issues should be fixed where they'll have the most effect:
1) In GTK+, fix all GTK+ apps 2) Workarounds in the themes (where there are already usually many app-specific hacks), fix all apps when that theme is in use. 3) Local CSS where each app has to individually fix the issue.