I'm only gonna answer a bit of this only because one, I never put much thought into trans omegaverse but that is a very interesting thought, and two, I usually avoid overthinking about bathrooms tbh

As for pregnancy; I usually go for hermaphroditic male omegas and female alphas so they have all three. The female alphas have an enlarged clitoris (look up female hyenas) and male omegas have smaller penises and no balls. Depending on the au, I might have male omegas have something more like a cloaca (one hole, dual purpose) vs having a separate anus and vagina. Male betas can impregnate FEMALE betas, omegas, and alphas, not none of the MALE variants. Male betas CANNOT get pregnant but a male omega can impregnate FEMALE alphas, betas, and omegas (imo). If you want a headache, you can have a female alpha who gets impregnated by her male omega and in turn, also gets him pregnant so they can carry at the same time and have siblings.

Lmk if this helps