for low power applications the engine build doesn't really matter. I highly doubt that these engines were perfectly tuned for automatic with X gearing or 4 speed with Y gearing from the factory. They just found a comprise in parts that would work well across the board.
If you are building a race car and you are looking for those extra tenths in 1/4 mile time, then yes you should probably be building out your whole drivetrain at the same time.