we need to be able to use different branches for the different releases of the ostree/atomic deliverables
Could you provide some more details here? The only place where git is used is for ostree configuration, and that should be configurable already: see config_branch here. Is this not enough?
config_branch
This issue has been migrated to Fedora Forge: https://forge.fedoraproject.org/pungi/pungi/issues/247
Please continue any further discussion there.