Overriding the settings file on 3020 should not be a problem. I know that at work on my Windows machine it is working fine. What platform are you on: windows, mac, linux?
As for accessing the default, I have just pushed a commit that allows for access to default settings via the menu at Preferences->Packages->ExportHtml.
As for branches, none of the main branches support ST3 at this time. I am waiting to see how Package Control sorts all of this out. It is way too much work to make these plugins (especially the complicated ones) support both ST2 and ST3. While possible, it may become pretty fragile, ugly, and troublesome in the future with new features etc. With that said, supporting multiple branches is also going to become tiresome as well, and I have full intentions to kill off support for the ST2 branches no later than the official ST3 release (if not sooner). While I won't delete ST2 branches, I plan on providing no future work on them either as long as they are stable. They may get moved somewhere else, and the main branch might just become the ST3 branch.