[release-1.8] 🐛 fix: considers objects in kube-system for cert-manager to avoid upgrading twice

[k8s-infra-cherrypick-robot]

This is an automated cherry-pick of #11351

/assign faiq

[chrischdi]

/test help

[k8s-ci-robot]

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[chrischdi]

/test pull-cluster-api-e2e-release-1-8

[chrischdi]

/lgtm
/approve

[k8s-ci-robot]

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[k8s-ci-robot]

LGTM label has been added.

Git tree hash: e92046e3599415c11ae343b434b1eea020995484

[fabriziopandini]

/area clusterctl