You should better ask the original author of the project about that, most likely somewhere there are event handlers that require additional clean up on scene change.
Also a noob question regarding best practice, when you use the destroy event does it clean up the events on scene change or do i need to use this.app.off somewhere too?
You always need to manage the event subscribers. If a script is listen to an event on the app object for example, it is also responsible for removing the subscriber when the script is destroyed.