Hi Uko,
If I understand your need correctly, I would say yes : you can add a spec repository: anUrl inside the version and this should override the repository inside the baseline method.
If you're ready to try some of the new stuff pushed in Metacello by Dale, I would suggest that you create a BaselineOfYourProject inside your branch and write a configuration which refer to the baseline; there, just changing the url to point to your branch would make it work.
inside the version method, for example: (gitfiletree url)
(It's also quite convenient to be able to work with metacello scripts which are as short as loading the configuration in the first place: