maybe in your isekai omegaverse au, reader does have a scent, but it's such a unique type of scent that it legit throws the hylians off? i dunno, ion read that much omegaverse fics.
SO! the plan is yes and no
reader has a scent, but it's not unique in an off-putting way. not completely
in omegaverse (at least how i'm gonna hc + think of it), scents help identify whether you're a/b/o, and the secondary gender determines your role in society (only to an extent tho. it's like ingrained instinct vs. will-power/desire/learned behavior thing)
but!!! we don't have that in our world. and tbh, i've seen people's roles and behaviors shift a LOT around different people, scenarios, places, and also phases of life
so i feel like you can kinda change yourself to be who you need to be (or who your close friends need you to be, given you're willing)
-> reader's scent can change
it might tend to smell a little subdued and not very strong, like who a beta would smell. but when caretaker/motherly/parental instincts start taking over, it shifts to be like an omega's. and in battle (? not sure if isekai!reader knows how to fight) or during arguments/heated situations, it flares and grows to be like an alpha's
it's got them all confused. but no one questions it because Four is also the same way at times. one second he's like a beta, and another like an alpha (i'm making him genderfluid to go with the colors). so they just think you're like him, whatever that may be
it's a sensitive topic for him, so they don't ask him about it. and they assume that it's something you might not want to talked about either
reality is you still don't know anything about scents lol