Germany has a small window in which it can afford to bolster its navy. Presuming the Russians are building a suitable wall in Karelia and the US and UK are planning to shuck-shuck, Germany needs every IPC later in the game to build infantry and armor and cannot afford to build a transport, sub, or (gasp) air craft carrier or battleship.
For that reason, Germany's only chance to improve her navy is first or second turn. Moreover, she must build it in the Mediterranean Sea, as attempting to build a navy in the Baltic Sea Zone is suicide given the proximity to UK and Russia's air forces.
Without that extra Mediterranean transport, Germany's options in Africa are limited (presuming the Allies make it a priority to eradicate the German navy). The transport buys a little insurance for Germany, an extra few turns in which it has to secure Africa and enjoy her IPCs before the Allies come storming into Algeria. And if the UK player is bent on building a South African factory that second transport is a requisite to have any hope in taking it out before enough of a defense can be constructed.
If you think this strategy works, what does it change about your first turn German attacks (i.e. presumably your med Battleship and Transport do not engage in naval battles, so how do you re-balance your attacks accordingly)?
Personally, I almost always use Don Rae's suggested first turn buying advice for Germany: purchase a transport and 8 infantry. Since this immobilizes my battleship and transport, I use a sub and fighter to off the British battleship and a bomber to nix the sub.
If those attacks fail, Germany is pretty much screwed, though. That's one thing I dislike about Axis & Allies in general - the first turn or two really has rippling effects through the rest of the game. A couple of bad dice rolls in the early game almost guarantees defeat, especially as the Axis where the margin for error is so narrow.