Currently, interplanetary spacecraft designs assume that the command ship will not be making a descent. That's fine - so long as you keep to your mission plan, there shouldn't be a problem.
However, this spacecraft from ??43 [We don't get a full date from the ship's log] would presumably have been capable of far more than current designs allow for. This vessel had been collecting things from all over the place - that implies something a little faster than a matter/antimatter reactor on the back.
Maybe it wasn't intended to make an atmospheric ascent, but if it needed to make a descent, perhaps it could have been given that capability. It did, after all, survive Earth atmospheric reentry.
I haven't actually seen the design of the ship, most of what I'm talking about comes from prior knowledge of space physics and my interest in speculative science fiction. If it is just a cylinder with a wing and a flag painted on that, well, maybe they thought it was a good place for a flag to go. With this spacecraft, I'll assume that the extra weight wouldn't be a problem.