Indeed, my reading of this is that the rule is not written for non-deliberate action by the batsman. The fielder didn’t throw the overthrow, it was caused by the interaction with the bat. So you can read it that the act that caused the overthrow occurred after the crossover.
Anyway, in the absence of clarity from the rules, the on-field umpires made a decision.
It wasn’t the last action of the match so both sides still had the opportunity to win the match. They then had this opportunity again in the Super Over.
Having said all that, it was an extraordinary end to a match and an even more extraordinary and wonderful attitude from the Black Caps to the defeat. I’d like to think we’d would have behaved in the same graceful way.
One might hope that Australian Umpires could learn from this, considering they come from a land where an underarm bowled ball was considered acceptable as the last ball of an innings in a one day match... or sandpaper in a pocket is a legitimate Test Cricket skill.