I also considered that possibility, that Wojoo was an omega from the beginning and there was a problem with his awakening due to the kidnapping.
It still doesn't justify Jiheon's obsession with changing his gender, although I do believe the kidnapping was what increased his obsession with Wojoo. The few childhood memories we've seen he was normal.
If that's the case then I feel it would mean Jiheon and Wooju have never know each other beyond Jiheon's obsession and this will be just another one dimensional abusive aob with zero character growth.
It doesn't justify it and it feels like the professor has latched into that obsession and using it to his advantage, it makes sense to try find someone who's part of the subject's trusted circle to provide the drug without this being suspicious and Jiheon's reaction to Wooju being afraid could explain why the experiment was previously stopped, but now the professor is back in Jiheon's life, Jiheon's feels this alpha is a threat and the professor feeds the paranoia by marking Wooju, now the need to tie Wooju has come back to Jiheon's mind.
with turning Wooju into an omega and he's using that to either carry on with some kind of study to get a drug like this into the market, or he wants Wooju too. Or maybe some kind of revenge against Jiheon or his mother.
But is really sad that for Jiheon his whole life revolves around his nature as an alpha, feels kinda like he refuses to know, care and love Wooju beyond their presentation as alpha and beta.
I would feel really betrayed if in the end Wooju is an omega who's ability to present was hindered after being kidnapped, because it feels like professor is just doing a follow up on an experiment.