I doubt anybody can tell you with absolute assurance that 6 inches lower than the factory install is certain to be OK, or certain to cause trouble. What IS certain is that the lower that loop, the more likely it is for water to be forced back into the water lift, and from there to the engine. Is the change significant? I am not sure, but....
If it was my boat, I'd insist that the yard make it the way it was, even it that required them to replace an expensive bit of hose they cut too short on the first try.
Edgertown, Martha's Vineyard