Open source is about taking back control over your software. The sentiment of that website is absurd to me. What I do on/to my own system is nobody else's business. (Though I don't really change much of the theming myself. Changed a few colors slightly and of course the desktop wallpaper.)
The sentiment still stands. I can't fault distros from wanting to theme their distro to match their branding. Like, Ubuntu wouldn't be Ubuntu without their signature orange and aubergine colors, Mint and openSUSE have their greens, and SteamOS' have their polished Vapor theme etc. And as an end user and a perpetual distro-hopper, I really appreciate that. I like the consistency that well-made distro themes provide, plus it makes you feel like you're actually using that distro, as opposed to some generic Linux with a vanilla GNOME/KDE shell on top.
Sounds fine to me, but these applications are already open source. If you're going to modify and repackage them, at least update the links to the bug tracker to your own.
The consistency is nice and all, but more than once have I seen distro replace a "stop" button with something they deemed similar enough that didn't make any sense in several applications that used them. I've also seen themes mess with spacing, hiding button rows or stretching them in weird ways. On a glance it all looks nice, but when you're using them applications look weird and broken.
Themes are nice, but unless there's an official theming feature (like with the new Gnome accent colours) it's the duty of a distro to inform their users that theme related UI glitches are the distro's fault, and I have seen none of them bother to communicate that.
In the mid 2000's, I loved trying different themes. These days I just take whatever is the default for Gnome, which is remarkably sane, usually more comfortable than a Mac, and consistent.
Some themes solve real problems, especially for the visually impaired, but that's not the norm. It's a fun work of art, but the utility is always limited. More often than I like to admit, I was left with a broken desktop after attempting to uninstall a theme that didn't work well enough (or at all), and that couldn't be fixed by installing another on top of it.
There are more pressing issues in Gnome than to provide a stable theme API.