There is more or less a combination of reasons for selecting 4.10 for autos and 3.73 for manual, I'd probably use 4.10 in either case. The reason that stands out the most would be the difference in 1st gear ratios, around 3.35 for the T5 and 2.40 for the AODE & AOD. Many feel that the deep first gear of the 5spd offers more than enough initial gearing when paired with a 3.73 rear ratio.
How much power the vehicle has, the weight of the vehicle, and other things would come into play when deciding what ratio to use.