Is the "auto-routing" created by online flight planning resources preferred by ATC over Direct routing when NO preferred route exists?
I did some follow up research and also spoke to an air traffic controller and I have a partial answer to this question. 


If the "auto-routing" doesn't make much "sense" and there are no "preferred routes" then the probability of "getting a direct clearance would be fairly high."
The "auto-routing" logic is simply using nearest victor airways from Point A to Point B. (I'm still looking for a source for this, but it seems pretty obvious to me now).