Thanks for your interest in Onboard and for helping us make it better.
Concerning your second point in your bug description: when Onboard gets manually unhidden when auto-show is running, the auto-show feature gets paused until the user hides Onboard again. This behaviour was intended by design. However, meanwhile, we wonder whether we should not also add a timeout to restart auto-show after it has been paused by a manual unhide.
Could you please give us more details about what you mean by "opening the dash" and "the right-click option to rename files in nautilus"? What is the relation to auto-show.
Finally, I think that it is fine to list all the applications that do not behave properly with auto-show in the same bug.