The default comparison can be changed in the user settings:
From the web client, click the "Settings" link in the tool bar, the select the Diff Viewer tab. Changing the "Default Version Comparison" setting will change which versions are displayed, by default, in the diff viewer.
However, this is contingent upon being able to clearly identify a base version - which may not be possible with addgitdiffs, as it allows for the upload of arbitrary files, absent any SCM indexing. They might try using addchangelist.
