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Matrix job by design require both head build and all axes to run SCM operations :
see for sample Git-plugin support for matrix jobs : https://github.com/jenkinsci/git-plugin/blob/master/src/main/java/hudson/plugins/git/GitSCM.java#L845
probably some SCM can do some light weight operation when they already know the revision to checkout, vs a full fetch from matrix head, but they will anyway have to do some stuff BOTH on axes and head.