To make the analogy work I think you have to assume he's referring to the complex of pipes hidden in the walls.
A messy unfathomable array of pipes will cause the plumber to spend more time fixing the problem and will cost the customer more.
A well arranged, "documented" set of plumbing will help a good plumber spend less time performing the maintenance lowering the long-term cost of ownership of the plumbing. Not only that, it's more likely to work correctly the first time. Instead of spending weeks calling out plumbers to figure out why no hot water is coming from the bathroom taps, etc.