That has nothing to do with GNOME. That's going to happen any time you try to theme 100 different programs and try to get them all to look consistent. Try to imagine writing one CSS and applying it to every website you visit and expecting it to work correctly. It's just not going to work, you'd have to manually rewrite the CSS for every site. The same is true of desktop applications. The only reason your desktop appears consistent with the default Ubuntu themes is because all the apps already did the work to target that theme. If you want another theme, you have to do all that work all over again. You can't avoid this just by adding more options, it's a large amount of extra code that needs to be written every time for every app.