If pkgset is skipped, it makes no sense to run gather. If gather is skipped, it makes no sense to run createrepo.
These conditions should be checked and an error reported if the requirement is skipped but the depending phase is not skipped.
Commit 4f96164e fixes this issue
Metadata Update from @lsedlar: - Issue set to the milestone: 4.1.40
This issue has been migrated to Fedora Forge: https://forge.fedoraproject.org/pungi/pungi/issues/1274
Please continue any further discussion there.