Arbitrary folder structures?

No, not by default but you can configure Blot to use the path to the file to generate its link. To configure this you will need a custom link format. You'll want to use the following custom link format:

{{stem}}

As for reserved top-level folders: in one sense, there is no such thing. You don't really need to create folders called Drafts or Pages or Posts, let alone Files or Media. You can create a draft inside the folder called Pages, a post inside a folder called Drafts, etc.

This is because metadata is what ultimately determines how Blot treats a file. For example, here is how you create a page using metadata:

Page: yes

Rest of the page goes here...

The file above can be placed anywhere inside your folder, and it will become a page.

However, Blot does treat some folders differently. For example, files inside a folder called Pages will have implicit metadata to the effect of Page: yes. The folders Blot treats differently are:

• Pages - files inside get Page: yes implicitly
• Drafts - files inside get Draft: yes implicitly
• Templates - files inside are used for locally editable templates

That's it! Writing this out has made me think I should clarify the documentation a little.