Well, adding extra impulse engines could give you extra speed and a little extra power for stuff. Although I'm sure they are not the most powerful impulse engines, but a little extra power might be useful compared to extra power needed to power Aft Photon launchers. And as SF2 had said, Mirandas were taking a beating during the Dominion War. Maybe Starfleet wanted to give Mirandas extra Power and Speed to survive battles. I'm sure if this was the case, only a few Mirandas received this kind of Modification.
And that was one thing I always scratched my head about aswell, how do they get thos Photons all the way up there to that launcher on Miranda's. My only guess is that Pod is automated and Mirandas had a more limited Magazine capacity compared to other ships of its generation.