I would go further, and contend that there are skills that are exercised in asymmetric two player starting positions that are not much exercised with the symmetric two player positions. The masterboard play can be much sharper when the first battle is likely to determine the game, as is likely the case before any of the four initial stacks have split.

I agree that in tournaments set up using single elimination rules, asymmetric positions can unduly penalize one of the players - though the same could be said for, say, unlucky rolls in key situations. The best solution might be to try to set up double elimination or Swiss System tournaments, and using the rules as written.