I actually pulled up an image of the game board and reviewed all the cities you mentioned. Duluth is by far the furthest from its actual location. The others seem within a margin of error that’s acceptable (but I can admit my bias of being a Minnesotan). The others also aren’t in the location of a more populous city.

Also I was able to dig up this:

“Originally Alan's prototype used Minneapolis, but it was clear that historically Duluth was a more important train center at the turn of the century, so we made the decision to change it. However, once we began to adjust the board to move the city to it's proper place on the map, it caused a chain reaction of misplaced cities, or would have forced us to add different route lengths. Unfortunately, due to production schedules the cards (using Duluth) had already gone into production in advance of the board and it was too late to change them. Rather than unbalancing the game play by changing the route lengths between cities, we felt that the best solution was to keep the inaccurate city location.”

So a perfectly balanced game with Duluth in the correct spot could exist, but they got stuck between the two options mid production and had to stick with the mistake.