If you change your oil often enough, I don't think it is necessary to run your bike prior to changing the oil. I never make a special point of doing that. It really means that you just take a bit longer to completely drain the colder oil. Once I change my oil, it seems to stay pretty clean, which indicates to me this works OK.
To answer your question though, the clutch and transmission's primary shaft do spin with the bike in nuetral (as long as the clutch is not pulled). The only thing that doesn't spin is the counter shaft. So your oil gets pretty well agitated while running in neutral.