The ability to run what you want and modify what you want is different from design freedom.

Indeed. Keeping people from modifying their software affects only developers, keeping people from choosing a theme affects every user.

The ability to use what software you want, however, isn't much different from the ability to use what theme you want.

And ultimately, freedom is not specifically about running the software you want, or about modifying software, but about doing what you want.

The ability to use whatever theme you want has created a situation where Linux UI is in complete disarray. If you want a different UI you should obviously have that option, but there isn't a major UI system that takes the opposite approach, instead developer effort is being wasted on a feature that's always broken all the time and restricted to handful of working themes anyway.

> there isn't a major UI system that takes the opposite approach

Good thing there is at least one then. Blindly cloning other "major UI systems", now that would be a waste of developer resources.