That particular deck for the Tamiya Yamato has pre-cut holes for all the deck fittings so you don't have to sand or cut off anything. Just drop the deck right on and everything fits.
The problem is the deck set is perfectly fitted for the Tamiya kit, and the Tamiya kit just isn't very accurate. If you try to correct some of the errors in the tamiya kit, or if you want to backdate the kit to sometime before Yamato's last voyage, then the pre-fab deck wouldn't fit anymore. They give you a small surplus deck piece so you can patch the deck set a little if you want. But that doesn't work very well because you can never cut the pieces as accurately as the manufactuerer. This is why I am planking the deck with wooden strips.
Planking the deck is much more labourious, and the final result doesn't look quite as good as the pre-fab wooden sheet deck, but it allows me to back date the kit to 1941.