If it killed the opponent first, a last-stock 200% Bowser could KO a last-stock 0% opponent, winning the match despite clearly losing... That would be too lopsided.
It would be the 0% player's fault entirely and they would deserve the loss, they basically have complete control of where Bowser goes in that situation. The lower percentage person has more control. Only "unfair" for players have no idea what they're doing, ie FG players.