Ok here is my take on the Cocytan Asteroid Ships:
They are designed to be un-manded, and automatic.
The actual ship (the dodecahedron part) is encased inside an asteroid for 3 main reasons. First to keep it safe and protected from random outside influence, simple as that. Secondly it is to 'soften the blow' to species that figure out what it really is, I mean was seems more soothing, a 'simple' asteroid with a few artificial chambers, or a giant, obviously complex spaceship? This sort of goes hand in hand with the third reason. If they can figure out what the asteroid really is and reach it, then the species is at a basic level to understand and accept alien life.
Now for Atilla and the new asteroid. It is my belief that it had been traveling for many many centuries before if finally made it to Earth. During this time it had in fact collided with many objects that had destroyed the original surface features. The new asteroid, having been sent directly to Earth had not had its surface destroyed in the same way, so it has an intact surface entrance. The reason that the Cocytians sent this form of ship again is for familiarity. The original three, for which the ship is intended, knows this form, and can speedily get in and activate it.
Now for the rest of my story, well that may have to wait for a bit. I have the loose story, but the details aren't set yet. But please feel free to keep asking questions, the more you ask, the more complete the story gets.