It sure would be nice if the SCM Skip plugin had an option to not skip builds that were manually triggered by a user. Currently, my declarative pipeline has to do:

script {
  if ( currentBuild.getBuildCauses('hudson.model.Cause$UserIdCause').size() > 0 ) {
    scmSkip(deleteBuild: true, skipPattern: '.*\\[(ci skip|skip ci)\\].*')
  }
}

... which is a lot uglier than with this hypothetical feature:

scmSkip( alsoSkipManualBuilds: false, deleteBuild: true, 
  skipPattern: '.*\\[(ci skip|skip ci)\\].*')

Note that I called it "alsoSkipManualBuilds" to avoid a double-negative; obviously the default should be current behavior, if you care.