The stopping of the timer has been changed from last hit on the final boss, to when you lose control of Bomberman. This happens when you hear the victory chime (and when Bomberman does his victory pose) after beating the final boss. This adds just north of 8 seconds to the run, so I have added 8 seconds to all Normal Mode runs.
So the question then is, why? Well it's never quite sat right with me that time stops on last hit, because unlike most other Bomberman games, you still have control of your character for a while. Worst case you could still die and then the question is "does it count?" Under the current (well old now) rule, because of the way the rule was worded, technically yes, but I feel like that's against the spirit of beating the game.
Luckily it's never come up for me but it's something I've always thought about. Once I have gotten hit after/as I killed the final boss but luckily I had a heart. I later learned that Super Bomberman 5 also is set to stop time when you lose control of your character so there is precedent. So I brought this up in the Bomberman discord and did not have anyone disagree so I went ahead and made the change.