Deck plate honing nearly duplicates the head bolt loads that cause distortion in the block when they are screwed in. By using the same gaskets, bolts, and torquing procedure, the cylinders deform like they would after the engine is assembled. After the plate is on, honing the cylinders makes them perfectly round again thereby eliminating blow-by and keeping the cylinder shape constant, improving efficiency and getting a longer life. When the engine runs, the block actually twists and deforms, and gets pulled every which way when all the components are screwed and bolted to it. By duplicating the loads that influence the distortion, you eliminate little inconsistancies, get a happier engine that will live a longer life. This is more important when pushing a design to it's limits. The higher the performance, the less room there is for error. This process is one that racers have been using for ions, and while these little inconsistancies don't effect the engine too much, when you're looking for every little bit of power, or looking for hitting a specific safety factor when you're pushing the envelop, this is one of the tools one can use to nearly assure the best running and longest lasting engine possible. If you've ever heard of engine blue-printing - this is an element of that process.
"...What IS true: We anticipated that this would happen - we are never finished - and yes, Ford DOES deserve to win now and then. To think that GM can come out with a car to make ford throw in the towel is simply foolhardy..." - fbodfather