God, that's such a specific question I had to re-read it twice. I think you're talking about the 'omega' being assigned 'MTF' as a separate concept? Honestly, I've seen a few fics that play with this crossover, blending Omegaverse mechanics with trans identity arcs, and it gets messy fast in terms of relationship dynamics.
In a lot of the ones I've read, the 'MTF' aspect often gets completely steamrolled by the omega biology. Like, the character's personal journey of transition becomes secondary to the biological imperative of heats, submission urges, and pack hierarchy. It can feel like the author just slapped a trans label on an omega template without letting the two identities truly interact. The alpha love interest usually ends up focused on 'the omega' part, which... yeah, problematic.
But there's this one series, 'A Scent of Truth' by Lee Winter, that handles it differently. The omega's transition is central; her dysphoria is sometimes amplified by the omega biology she didn't choose, and her alpha partner has to navigate supporting her gender identity while also dealing with the biological pull. It makes the trust and communication aspect ten times more intense. The dynamic becomes less about dominant/submissive and more about negotiated care, which is actually way more interesting.
It’s a niche within a niche, and most attempts fumble it, but when done with care it adds layers you just don't get in standard Omegaverse.