That’s wildly incorrect.
1) At the time of the founding, the free-state/slave-state dichotomy was almost perfectly orthogonal to the big-state/little-state dichotomy. The plan for proportional representation in both houses was the Virginia Plan.
2) The Missouri Compromise had nothing to do with California being one state. When California was admitted to the union, it had significantly less population than South Dakota and North Dakota did when they were admitted to the union. The subsequent growth of California was an accident of history.
3) State boundaries are absolutely meaningful cultural boundaries. My wife is Oregonian and I’m from Virginia and we’re really different. Even the blue parts of both states are very different.
Also, we have freedom of movement in this country. The precision of the state boundaries doesn’t matter so much given that people can self select to the states that reflect their values.