Tableau uses # only for the base site that is for the default site. When you add a new site, you can specify the site ID. Other than the default site, Tableau uses #/site/Site_ID
For example, in our environment we have site called IT. So, it is identified as #/site/ID.
Hope this helps.
It's the /#/site/ part that lets you know you are not in the Default Site.
This is the Default Site for Tableau Server: http://myServer.com/#/projects
This is a custom Site: http://myServer.com/#/site/area51/projects
This is another custom Site: http://myServer.com/#/site/fidat/projects
The Default Site URL cannot be altered:
Adding a Site will not break anything
More here in the Admin guide: Add or Edit Sites