You may actually be right..
Actually as crazy as this guy is, (Plutonian not Waid or Millar..;) ) he might have done exactly what you proposed in your 2nd suggestion..
Might even be deliberate, as some kind of twisted version of Superman's penchant for making up replicas of people in his fortress of solitude back in the day..
(Or even Bat's Robin Uniform 'trophy' case..)
But yeah, I'm still smarting over where Millar left Doom at the end of his FF run, so I can see what you're talking about in your comparison there..He doesn't seem one for thinking through the long term consequeces of his plot twists..Cough! (Civil War) Cough!
Still I'm trying to remain hopeful that Waid on the other hand, might be soon pulling it all together. But I guess we'll see soon enough whether he's thought it all through..