Why filesystem-hierarchy is forbidden as a tag?
Is not forbidden. Forbidden tags are blacklisted.
Why can't the tag exist alongside filesystem?
Let me turn around your question: Why do we need another tag if there's something that already covers the same topic?
SE don't like to create a tag if there's another that covers exactly the same topic unless this topic has enough questions to do a topic on it's own (think javascript and jquery). This also decreases the possibility to get your question answered. So, it could be counter intuitive to create a single tag over selecting the one that has 20 followers, no?
Is the former too minor a tag to have a separate identity (even in Linux!)?
We barely get 1 question/day in the filesystem tag and not all of them are answered. There isn't enough traffic that could explain the need of a second tag and separating it reduces the opportunity that those questions get answers.
Do we want our tags to be general or specific?
They should be useful. We don't need tags that summarize the content of the questions, nor that could be too general that almost any question would fit.