Using the fzdefaults.xml file we were able to add a pre-configured server complete with authentication. The trick that I found was the <Logontype> had to be changed to 1 in order to use normal authentication. As well the Name of the site is set after the <RemoteDir></RemoteDir> entry. I was pleasantly surprised that the pre-defined server shows up in FileZilla Site Manager in a separate section and is not editable.
The section in fzdefaults.xml looks like this:
<RemoteDir></RemoteDir>FTP Site Name
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