I agree 100%. In development there’s always a trade-off between resources you have and the features people want. I was just commenting about how it was technically straightforward. However it may never get done (understandably so) due to trying to balance ever-shifting resources, feature requests, bug fixes and existing development already in flight.
Why not give the user running the EN application whether to actually log out or not? Under "Option" -> "General", you could add a checkbox saying "Automatically log out the current user when exiting Evernote". When the user closes the Evernote window, EN can look at that checkbox. If it's checked, perform the operation File -> Sign out User then File -> Exit. If not, the just File -> Exit. It isn't that hard unless I'm missing something.