I don't know if the LTL question will ever be resolved to an auditor's true satisfaction. In the past, I relied on having my receiving checklist focus on the package integrity itself as an acknowledgement that we cannot control how the LTL companies handle the product out of our sight/control. So long as actual cross contamination has not occurred, odors are not noted as permeating your product, and package integrity is intact, one can deduce the food safety aspect of the received goods remains intact. That said, anyone shipping food LTL should be ensuring pallets are secured in wrap with tamper type products.
One auditor suggested we should be rejecting LTL pallets if they're stacked next to motor oil or poisons, or refusing to load LTL's that had questionable materials on them. That made no sense to me, knowing that LTL trucking companies cross-dock everything they transport at various hubs. It's perfectly likely your food was sitting next to God-knows-what before they loaded it onto the trailer to bring to you, and just because you manage to see it stored next to something bad means it should be rejected? Not in my mind. You cannot control where that truck goes after picking up with you either, so the lock is somewhat pointless knowing the forklift operator at the next stop will be parking right next to your shipment.
Now, if they deliver your packages and they're covered with spilled peanuts and rodent droppings, absolutely reject the load for mishandling. If they beat your product to smithereens, and package integrity is compromised, reject it.