Actually the ship itself existed for a long time before it was renamed. Talon would probably be the best person to get specifics from regarding this, but I'll relay what I know.

The ship was originally commissioned as the Mustang and was renamed Atrus much later (possibly as much as years later, I'm not sure when the Mustang first showed up). It has been the flagship of the Vast Empire for as long as I (and probably the majority of our active members) can remember. It has usually been captained by the current NCC, though others have been designated from time to time. It has had prominate roles in most of the major VE chapters (that I've read).

It is "modfied" from the normal SSD with a few different things, most of which I can't recall. Other help will be needed, I'm sure. What I do remember is that it is equipped with a large number of drone TIE fighters and the necissary equipment to control them. Any other changes will need to come from someone else, as I simply cannot recall.

Hope that helps, I'll try to throw more out there if it comes to me.