I'm thinking the goal was to cancel out the opposing forces of the moving masses. If you have two woofers firing in the same direction, in phase, then your sub might have a tendency to walk. Or jump if the woofers are mounted vertically-firing.
What you saw was likely a "push-pull" alignment. In other words, the drivers were both firing out of the box, one was just reversed and phase switched, so it was pulling while the other was pushing.
Other than potentially being a little ugly, opposed push-pull alignments have the distinct advantage of largely cancelling the 2nd harmonic distortion inherent to some degree in all drivers.
Every driver has asymetries in its motor's magnetic field and suspension's compliance. This means that inward excursions will differ from outward in terms of force over distance. But when two drivers with identical asymetries operate in opposite phase, the asymetries cancel each other in the net output.
Since well-engineered drivers minimize these asymetries, they benefit less from push-pull alignments than poorer drivers do.
However, strictly from an aesthetic point of view, if you paid a bunch for a pair of really nice drivers, you might as well show off the big ol' motor of one and the cone of the other! The slight distortion reduction would just be a bonus in that case.
One more thing: if a driver has a lot of suspension or vent noise, it may be counterproductive to mount the motor outside the box.
Chuck, are you sure they weren't passive radiators? That could be another possibility. I've seen Adire subs, where the sub is down-facing with PR's in the front and back. I don't mean to question what you saw, but PR's can have the same appearance as a sub from the outside.
Okay, now I realize I didn't read closely enough. Out of one side, into the other. Bill's post helped me realize my mistake. And he's right - this set up will cancel the even-order harmonics. Though IIRC the even-orders are supposedly the pleasant sounding harmonics - its the odd-orders you'd prefer to eliminate.