Earlier quoted context omitted.
gnome breaks userspace, kde breaks userspace etc. skype is not just linked against the kernel after all, but a whole lot of different components
Gnome and KDE run in userspace. They are desktop environments, they don't "break userspace". I feel like you're talking about GTK and Qt, both of which (don't break userspace either) are libraries you can statically link and nothing will break.
sure you can have bunch of ifdef in the code, and an autoconf, and make sure you support a wide set of options, but that is basically the whole point, it makes for a painful experience and costlier, slower development (for closed source application that comes prepackaged)