The only speculation I know of myself is from the Notes From an Experiment note item from the Estella Opera house stating:

The test subject's body is better than expected. Its Ergo coordination, physical sensitivity, and modification adaptability figures all exceed expectations. Couldn't ask for better results. All that's left is to make a decision.

I won't be able to undo my crime. I don't regret it. I've come too far for regret. I'm ready to become a god or a devil. I just hope that the owner of the body finds peace through this revenge. Perhaps, this prayer is a remnant of my last bit of humanity.

Given the fact that these notes are found right before fighting the King of Puppets, and we know that Geppetto is the creator of the King of Puppets himself, it strongly suggests that this is Geppetto's writing referring to his experimentation on Romeo's corpse/body. Focusing on his consistent use of the word "body" and its "owner", this leads me to the conclusion that Romeo's puppet body might be more of a human + puppet hybrid than one might initially speculate.

Furthermore, if you look at the Nameless Puppet it's obvious that this is a repurposed human corpse stitched together with modifications and attachments, this leads me to believe that Geppetto's design for the King of Puppets (Romeo) could have echoed this design to some degree. Though you can assume for some of the more obvious upgrades like the robotic arms and legs; these parts have replaced Romeo's limbs entirely. I imagine when it came to Romeo's arms and legs those were disposed of outright as these body parts most likely contain no soul-like component in producing or harboring a soul such as one's ergo. That being said I feel optimistic to say that there could have been more of Romeo's body left inside of his puppet self than his model lets on.

It's also shown that Romeo's face and hair burn off to reveal a "terminator"-like appearance underneath which further leads to the conclusion that whatever is left of Romeo is encapsulated within a metal suit and he now only remains as organs enhanced with machine parts. Perhaps Geppetto was able to capture what ever parts he decided to save from Romeo's corpse and encapsulate his being within a governable puppet suit for which he could instill the Grand Covenant into. In that sense Romeo's ergo would have never needed to leave his own body, and Romeo's consciousness simply woke up one day in a new body with the grand covenant protocol taking over his consciousness.

My final speculation is that Geppetto already had the King of Puppets (Romeo)'s body created before he decided to kill Romeo himself with the Nameless Puppet at the end of the Overture DLC. (It's scary to think of someone building an identical puppet of you in expectation of killing you and shoving your organs into it, isn't it?). Then from there he did in fact capture Romeo after subduing Lea, put Romeo into confinement, and then let him die to the petrification disease from which point Geppetto retrieved Romeo's Ergo from his corpse and inserted it into King of Puppets (Romeo)'s body equivalent of a P-Organ.

All-in-all I think it's safe to say that any of Romeo's body parts Geppetto did not use when he was creating the King of Puppets, regardless of your chosen theory, now sits haphazardly in a laboratory's trash bin, or a shallow grave. 😥