This is a difficult problem for me to resolve.
My knee-jerk instinct is that identical opening splits is a simple and sensible tournament variant of the game, in the same way that most competitive video games have different rulesets for competition (see, e.g., SSBM, Starcraft, TF2, Halo).
On the other hand, players are free to alter the rules if they mutually agree, and the default rules that we impose ought to be the rules of Dominion as written.
My ultimate reasoning was grounded in the fact that this default rule comes into play only when one side insists on it and the other insists on the other. These situations seem likely only to occur when one side stands to gain some sort of advantage from the variance (e.g., a player is significantly worse), and in such situations I'd hate to be siding with the player seeking an advantage through random luck. I have no problem with -- and indeed, encourage -- players to decide on their own to abandon identical starts.
But I'd love to keep hearing all your thoughts.