The rod is not going to touch the chalk mark in any view unless you want to skewer the agent representing JFK. I don't know why you have a problem with what Specter did.
The rod being above the chalk mark in the left view makes no sense to me. It does not fit with the sworn testimony of Shaneyfelt. It make no sense to raise it above the chalk mark in order to represent the correct lateral angle of the path of the bullet through Kennedy. That's why I asked John Mytton if it could be a photographic perspective issue that we're dealing with here.