performAllBuildSteps(listener, project.getPublishersList(), false) is called twice in "Build Flow" projects leading to problems like duplicated mail sending.
Commit 89a9037 changed the base class of BuildWithWorkspaceRunnerImpl from AbstractRunner to BuildExecution. Because BuildWithWorkspaceRunnerImpl.cleanUp calls super.cleanUp (com/cloudbees/plugins/flow/FlowRun.java:204) this adds the cleanUp from BuildExecution on top of the cleanUp from BuildWithWorkspaceRunnerImpl.
If the only goal with commit 89a9037 was to get rid of the deprecation warning then the easiest solution is to extend from AbstractBuildExecution instead of BuildExecution. This will give the exact same behavior as extending AbstractRunner but without the deprecation warning.