I think this partly boils down to cultural differences. In Linux(Gtk+, Qt for example), global themeability has always been the way of doing things. Instead of designing the graphics for the user interface elements the coder just uses generic widgets like buttons, toolbars etc. The look of these generic widgets is defined in the global theme. The advantage of this is consistency. You don't have to theme each application separately, they automatically inherit the graphic design. Why people are so allergic to the word "custom" is that the custom elements can't be themed like this. If you designed custom UI graphics with light colors, no matter how nice it looks, it'll look out of place if the user wants to use a dark theme.

In my opinion, this can sometimes make the user interface look a bit boring. Applications mostly look like each other and it's difficult to distinguish them from each other at a glance. It's difficult to use different kind of graphics for applications of different purposes. In my opinion it'd be nice to use a bit more colourful and blingy graphics in entertainment software while office software could look more conservative. But I still don't want to lose the ability to theme globally.

Maybe a middle ground could be the best option? Maybe more widgets so that you could choose from a bunch of button styles the one that best fits the look and feel of your application. A bit more variety could help make the UIs more vibrant while still having them themeable globally.