M&K push/pull sub woofers work this way, and indeed my own sub is similar to this. The reason for it in this case, is that this particular type of sub requires one drivers motor to be outside of the box, and having it on the bottom is just the most practical way to hide the ugly bit. In honesty though, I couldn't see a specific reason to do this with both drivers mounted traditionally unless the box dimensions leant themselves to this as preference.I have never seen a system with one downfiring and one forward facing, but sure, I suppose it could be done.
This would be best for the cabinet. It doesnt really matter for the drivers. With one face holding the driver(s), as a driver pushes forward you get an equal opposite reaction from the box. The box is heavier so wont move as much as the driver, but you can still get some if the box isnt heavy enough and the driver is strong. By putting a second driver in the opposite face you cancel out this movement within the cabinet, generally making everything better. With no movement from the box, your also making sure there is no minor cancellation occurring so your getting the maximum output from your driver.Alingment I guess you mean would be one front and one in rear