In 2.15 of the Pipeline Multibranch Plugin the feature Option to select a script name/path other than Jenkinsfile. was added as part of https://issues.jenkins-ci.org/browse/JENKINS-34561.

Adding multiple workflow recognizers should be supported in the OrganizationFolderJob DSL in something like the following (using WorkflowBranchProjectFactory as an example of an extensible context):

organizationFolder('folder') {
  projectFactories {
    workflowBranchProjectFactory {
      scriptPath('.jenkins/Jenkinsfile.groovy')
    }
  }
}