Not 'skins' per se, but even when themed, most (good) professional apps will still use native or native-behaving controls and similar design language to the host OS.

In comparison, Mac apps will look and feel different from Linux or Windows apps, and QT and GTK+ apps will look and feel different from one another or the other two.

Switching between apps, even with heavily customized UI/UX, is consistent on a given platform, and that's what's important. Taking that away will just frustrate users and complicate things overmuch.