It’s been mentioned that Machia didn’t even need any modifications. Also, it’s not like doctor’s aim was to turn all the people into “the perfect beings”. He’s not this altruistic. Tomura just happened to be a successor of doctor’s friend/idol/you name it, doctor clearly stated that “he lived for Shigaraki’s sake”.
Also, don’t forget that the laboratory has been destroyed. And all the quirks stored there were destroyed. And the machines needed for quirk duplication/transition/so on. And the doctor is caught by the heroes anyway. And, in case Tomura gets defeated (or even if he wins, but they en up separated) - there is a good chance that AFO (as a quirk) is still needed to produce anything momu-like, as doctor has mentioned that after AFO got caught, the process of creating nomu became extremely hard and troublesome. It’s highly probable that this quirk is also needed to create the duplicates of quirks.
Also, it seems like the first phase of the whole operation of turning a normal human into a god-like one (like Tomura now) is painful enough to render them completely mental, just from sheer pain. Let’s say, Tomura somehow managed to endure without losing his sanity, but he’s pretty special anyway.