I love Linux based operating systems and I've used them pretty much exclusively for at least a decade now, and I agree with a lot of your post, but
>By cutting away abstraction,
I don't think I agree with this take. You haven't cut away abstraction, you've changed to a different kind of abstraction. Linux's 'everything is a file' abstraction is just that, an abstraction.
>Linux is arranged masterfully, and makes the Windows filesystem look like a joke in comparison
It's arranged more simply and straightforward, masterfully though, I dunno...
Every flavour of Linux uses a different layout for its root directories, stores configs in different places and generally is not consistent from distro to distro.
User configs are also scattered in random places at times. They could be in .config they could be in .local they could be in .$APP_NAME they could be in the app's directory, they could be in /usr/ somewhere. Maybe in a couple different places at once. Who knows? It's a mystery until you track it down.
Dependencies and libraries are a huge pain to deal with, especially when you start mixing and matching distro provided libraries with custom built ones.
I'm not trying to disagree with your post or anything. I love the way Linux lets you have control over your computer and doesn't try to stop you. But, it's definitely got some issues. I've only touched on a few related to your comment itself.