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couple years back, there was a thought that the bolt was a thread or two to long. Thus bottoming out and not allowing proper torque.
To achieve proper torque, the bolt can NOT bottom out while torquing. And final torque must be achieved and read, while bolt is still turning. Plus new torque methods say torque to xxx number of pounds (etc), then tighten xxx number degrees past that point.
So I would measure total hole depth and compare that with total bolt length.
Then if bolt is too long, I would grind it down the one thread (have done it lots on head bolts etc). Then use the proper thread lock.
But that is me, you do it your way.