First, I know the difference between sub-domains and sub-directories, and the reasoning behind using both. This is not that question.
My question comes from the way that my host (he.net) treats multiple domain names on the same account. I have a site hosted at example1.com, stored in the public root directory of my shared hosting account. When I add an additional domain to my hosting account, example2.com, the host creates a sub-directory within the root, titled "www.example2.com" and sets their server to direct queries for the new domain to that sub-directory.
Now, I'd like to use a sub-domain network, and my hunch is that I can do this, regardless of the setup I've described above. In fact, I wonder if I could skip adding the domain to my hosting account (and bypassing their server re-direction to the "www.example2.com" subdirectory), and just add the domain using the domain mapping plugin.
Thoughts? Is there anything I'm missing?