I suppose it depends on where you see it operating,
If it's on the edge or away from the asteroid field then the separator and hab modules sound good.
If you see it in the middle of the roid field then out of respect of the fact that stray roids will probably bump and damage it from time to time then to me it would be best kept simple and used more to do 1st stage work so perhaps an internal crusher, means of directing the crushed rock into the different loading tubes and thats about it, just to keep it relatively simple to fix, in this case I would go with the piping in the recess and perhaps have a docking point extending from where you are thinking of putting the hab complex so a ship can dock onto and move the installation when needed, either to avoid danger, move it to a more economical locations or for repair.