"The parts you put on these ships, at launch, will have no aesthetic visuals on the hull itself.
We may make each Mark have a slightly different 3D model and texture to represent their specialization."
That idea doesn't sound too bad actually. Not sure if anybody is familiar with EvE Online, but there is a class of ship called Strategic Cruisers. They all have the same base hull and function, but they can be specialized for certain roles and the hull shape changes accordingly while keeping the "soul" of the ship intact. For example, they each have different propulsion system modules you can mount and they provide a different aesthetic look to the rear end of the ship. The Tengu (one of the ship classes) may have many different setups, but you can still tell its a Tengu. Video below to show what I mean.
Skip to :40 to skip past the EvE related stuff to the ship fittings.http://www.youtube.com/watch?v=JvqNLGsgV98
I don't know if you want to go that far with the physical alterations, but for the Mark I or Mark II for example could have a clunkier, beefier look with some additional external armor plating on the front and sides or for the Mark VI add more secondary engine clusters to the back of the Mark V model. I would be just as satisfied with these little model changes as I would be with a complete spaceship build-your-own burger type of deal. That would be fun too :p