We are using Organization plugin and Jenkinsfile to override some of the repo/project level settings. One of them changed the build behavior to not trigger master branch buiilds automatically and instead run then on schedule.
After upgrading Branch API and installing Basic Branch Build Strategies plugin I started seeing this error on the Job Console:
ERROR: cannot apply jenkins.branch.OverrideIndexTriggersJobProperty to a WorkflowJob
I don't see any other way right now to change project level settings.