Seems plausible.....good theory.
Plot twist could be the Dr knew puppy-kun since school. Like maybe he was a senior and was behind people finding out about puppy-kun cross dresssing and ostracizing him. All this while he’s been stalking puppy-kun and destroying all his relationships in a bid, as you said, to have him depend on him alone!
I agree with your theory. I don't like the seme. He's a typical manipulative sadist. this is not healthy BDSM at all. He knows how vulnerable and fragile the uke is and is highly taking advantage of him
The seme is behind all this and is just trying to manipulate the sub into dependency by first abandoning him, then making him feel vulnerable and finally pretending to be a good worried Dom. That's my theory.