So as far as I can tell, in the WR run, the timer is stopped before CH actually gets the last hit on Dedede (by at least 1 second). Obviously, this was not a cheat, he just accidentally stopped the timer early.

it's offset because of the delay. you'll notice that the timer starts before the run does. It's most definitely a legit run

The game and timer were not in sync, there's a delay.

Okay, sorry for confusion.