Three minutes may not get the oil to maximum temperature, but should get hot enough expand some. Thats probably why the manual says "between the L and F mark". Allow for a bit more expansion if its going to happen.
In any case, the 650 takes 2.7 liters w/filter, so I just put that much in and go for it. (Yes, I have double checked in the sight glass, and that comes to exactly on the F mark.)
But to the point of the original post, something was done wrong at the shop. I would request a complete check, including compression test and oil pressure test, at the shops expense.
I don't want a pickle, I just want to ride my motorsickle. A. Guthrie.