If 'skipDefaultCheckout' option is not included in Jenkinsfile pipeline definition then pipeline job will trigger a full SCM checkout. This makes no sense when lightweight checkout has been ticked because the user only wants the Jenkinsfile(s).
Would be good if 'skipDefaultCheckout(false)' is the default when using lightweight checkout or provide a tick box on the job configuration page to set it (under 'Lightweight checkout' tick-box).
skipDefaultCheckout is unrelated to lightweight checkouts - it's for when you're entering an agent, while lightweight checkouts are run on the master in order to get the Jenkinsfile in the first place.