I installed my 460 loader myself and the rod fits flush with the tube when level, never cut it. I had always assumed this is the way they were meant to be since every backhoe I have ever used worked the same way.
Come to think of it, our old NH 1720 (7308) loader manual also said to cut it off flush but the dealer delivered it long. I tried using it with a mark on it for a while, but it was too hard to see when it was dark out so I ended up cutting that one too.
Jay