Of course changing the tire size has an impact on the transmission's ratios. This is the reason why when you put a 4.88:1 on the differential and you keep your stock gear set in the gearbox you end up with a 300-500rpm increase for cruising at 75-80mph. If you want to get back to say cruising at 2200rpm for that speed instead of 2700rpm, you need to have more gears in your gearbox i.e. a second overdrive. So another progressive step in the system to get back to stock configuration.

You are correct it is expensive to have a customizable gearbox; but it is hardly not worth it.