At this point they seem totally legit and the MC is turning into an omega. There's always a slight chance it's something else, like they triggered the MC's delayed manifestation or the ML is secretly an enigma, but this doesn't seem to be one of those ones where the pills were a lie.

ML having been in love with the MC for ages and MC just not remembering him or something.

MC is like, huh, I feel hot but don't have a fever. Huh, for some reason I really want to smell ML's pheromones. Huh, why am I getting so wet and h**ny? What in the world could be happening to me, someone who is supposed to manifest as an omega any day now?

Like there's no way he wouldn't know some of the warning signs of a heat, even if somehow there was no education on it, it would happen sometime around people since there seems to be ways to have it not be completely predictable or it would be in movies/tv shows/books. Betas especially are probably told how to tell an omega is in heat since they can't smell pheromones and may need to get someone help or something.

the ML realized he'd confined the MC in his apartment and never even asked what the MC likes to eat or do or anything.

The confinement itself does make sense, as the MC can manifest as an omega at any time and not know how to control his pheromones or anything. But MC basically has no communication with the outside world, is forced to eat whatever and however much the ML was eating (like if the ML has a single piece of toast for breakfast, that's all the MC gets to eat until lunch), and there's a bunch of other pretty ridiculous restraints when the entire reason MC is confined is supposed to just be to protect him/keep him from physically interacting with people.

He finally asked what MC likes for breakfast (literally not at all what he'd been preparing), but... pretty much only improved on very small things. Like it was this huge revelation to him and... he didn't think about how what he found out might extend into other things.