If GTK3 still does not support theming, that explains why theming causes issues. In which case it would be better to implement proper theming support because stopping distributions from theming clearly doesn't work.

Oh yes, people have always done it, via one hack or another, and as long as it was more of a "for people who really want to fiddle" it wasn't that much of an issue.

But now expectations have risen, people expect more solid behaviour and look/feel from their apps, and distros routinely have quite different GTK themes.