Fully threaded socket head cap screws - are they supposed to screw flush?

use a parting/ grooving tool in the lathe and very carefully clean up the area of the thread under the head of the screw. I do it a bunch as screws are pretty crudely formed and the heads are rarely concentric with the threads.
 
One could machine off the threads on the bottom so they will seat if that is what is required.
 
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