My understanding is that it was largely as a way to appease slave states and provide reassurance that there wouldn't be abolition at the federal level, not to provide an idealized balance between states.

And even if it were for that purpose, having a "winner takes all" that requires 51% to achieve would still be better than the current system, which still allows for a winner-takes-all state but with much less than 51%. Checks and balances were designed under the assumption that the legislative, executive, and judicial branches would be balanced by a constant struggle against each other. They didn't account for political parties, which can result in multiple branches of government being controlled by an overarching party, effectively negating those balances.