Why boarding Yamato would not guarantee her capture

Could Yamato have been scuttled quickly enough to defeat an enemy boarding attempt?

Probably: deliberate flooding could make the ship untenable, while disabled closures and magazine demolition charges would deny a prize crew the chance to save her.

Opening sea valves alone would not make a battleship disappear immediately. The defenders could accelerate flooding by opening internal doors and disabling the closures or pumps that a prize crew might otherwise use. Water entering fast enough could still force boarders to evacuate well before the hull reached the bottom. Japanese officers could also use magazine charges as a more decisive denial measure, making an unwanted capture of Yamato highly unlikely.