Apparently some of these "it has to be that way" and "you can't do that" comes from internet hype passed from one person to another. That's the only conclusion I can come to as to why everyone says it affects the timing, but no one really knows why.
I am still open to the idea that it may affect the timing, but I suspect there is a + or - length that still works. The factory threw these engines together on a assembly line, and everything has a tolerance. The position of the camshaft lobes, the locating pin or keyway on the gears that drive the cam and the pump, even stuff in the pump itself have + or - tolerances. As long as these components are built within the "window", they are considered good enough for the engine to run. I am sure most of you know what "blueprinting" means, trying to take out these factory tolerances and bring them in as close as possible.
I would suspect there is a length tolerance on the injection lines where they will work ok with little noticeable affect on the engine's performance, but I am guessing about this and still don't know for sure.