On our old front door that we recently replaced they were on the same side. At our previous house the original door had them on opposite sides. So you’d open the storm door with your left hand and then have to reach toward that door jamb to get to the knob of the front door. It was a pain in the butt when I had my hands full.
They're opposite each other on our back door. In our case it's because of door swings- if the storm door matched the back door, the swing would block the direct path to the stairs off the deck, if the door matched the storm door it would be awkward going into the kitchen. It seems weird on its own, but makes sense in the space.