I hope you have Advanced AI enabled in the options otherwise the mod will use vanilla behavior.
One of the source of issue you have is simply too high speed limit on roads across the city, so they may choose a bit slower road but the route is significantly shorter. Time to stop or accelerate to max speed is not taken into account when searching for path, so route through many intersections might not be considered as bad as it would IRL

Another possible fix is to use Transfer Manager and switch Vehicle Pathing to 'Path Distance' instead of 'Line of Sight'. This way, vehicles will prefer the less circuitous path of the highway to that of the convoluted city grid, even though the LOS distance to their destination is shorter when looking straight across the city.