Sure, much of these are abstract things which could end up with you doing the same stuff but a different way. But I find that changing a path in front-matter is less painful than moving a file. And I can put a thing in multiple paths.
I use the Obsidian Zettel note to automatically name the file and I shove them all into the same directory. I then use the Dataview plugin to run queries for what I need.
I have MD files strictly for navigation, as if they are part of a static site layer. These files contain the links to go further into the navigation. It's basically all index files.
I keep everything together in the same vault, because so far I don't see a need to do any different. I just want to be able to navigate through the thing so that I'm not seeing a bunch of unrelated junk to distract me.
I do use directories to separate very different types. Like PDF's and Epubs go into one directory. Images go into another directory. MD files go into another directory. I don't know that I even need to do this, but I haven't run into a problem.