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:
<Servers>
<Server>
<Host>servernameORip-address</Host>
<Port>21</Port>
<Protocol>0</Protocol>
<Type>0</Type>
<Logontype>1</Logontype>
<User>username</User>
<Pass>password</Pass>
<TimezoneOffset>0</TimezoneOffset>
<PasvMode>MODE_DEFAULT</PasvMode>
<MaximumMultipleConnections>0</MaximumMultipleConnections>
<EncodingType>Auto</EncodingType>
<Comments></Comments>
<LocalDir></LocalDir>
<RemoteDir></RemoteDir>FTP Site Name
</Server>
</Servers>
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