Well, their HO stuff has a single horizontal motor, I see no reason as to why the S F3's wouldn't be the same. Supposedly the new PS3 board was developed for the F3's and adapted to the O scale 44 tonner.
Regardless, good performance comes from the quality of the motor and gearing and not the position of the motor.
Still, I'd rather deal with 3 motors in an A-B-A set instead of 6.
Rusty