Turns out the shuttle isn't a Kodiak; it's just a new type of Alliance troop transport. The pilots simply like flying upside down in an atmosphere. Hopefully after their team has geared up, and then locked themselves back into their safety harness, do they do this.
For the part of the anime that has some value, dramatic or otherwise, that is, Vega's choice, I still wish I knew 1) why and how the Collector Cruiser crashes into the planet, 2) how they actually saved Tria, and 3) how and why they ended up in the atmosphere. Without showing or explaining why those things happened, the value of the choice -- it's believability -- is circumspect.