If they are both in 3rd gears, its a 1.64 vs a 1.33. Of course these is going to be a difference between the two.
In practical application, the closeness between 3rd and 4th in the 6speed means that I often find myself skipping 3rd all-together as I dont need it for much. If I were racing, it might be beneficial to eek out each gear to keep it in the torque curve. However for everyday use its honestly just as well to have the 5speed.
My guess is that it would be cheaper and easier to simply swap out ratios and keep the 5 speed vs grafting in the 6 speed.