AFAIK, AutoEndTasks triggers only for non-responsive programs/routines. For example, you have an unsaved notepad - when you log out the process will ask you to respond within 1 minute (I don't remember exact interval). FSLogix Compact routine will be active while doing something so I don't think enabling AutoEndTasks will be an issue. The reason I say is because in a production environment customers might have log out script configured which sometimes might take more than 5 minutes to complete - in this case Windows cannot simply say - "Hey - I have AutoEndTask configured so I need to end your script" - lol.
Thanks for highlighting AutoEndTasks, btw. Now there are several other registry entries that need to be checked on Session Hosts such as WaitToKillService and its timeout value (specifically for Microsoft Services - since FSLogix belongs to MS Service) and WaitToKillAppTimeout, etc...hummm.