(Opening this to keep a record, but please consider low priority/"nice-to-have" because I understand the issue and have a work-around. It may be incidentally fixed anyway, or go away, if/when we fully transition to git)

If a local checkout has used both git and git-svn, the revision in vtkSlicerConfigure.h tracks the last git-svn update. This is because FindGit.cmake sets variables from git-svn after git. This can be problematic (and confusing) when the revision number is stuck at the same number as an already-installed nightly which has set some incompatible library paths set in the Extensions-####.ini file.