they can technically have sex. the only difference is that the omega can't knot him nor can he impregnate him. biologically, omegas generally prefer to get fucked rather than fuck, and an alpha's pride simply wouldn't allow it. however, there is actually a manga featuring an omega wanting to be the top with his relationship with his alpha. idk if it happened cuz the updates haven't really gotten to that part yet. (I can't remember the name tho..)
http://www.mangago.zone/read-manga/boku_no_high_spec_kareshi_sama/
It's this one. And he will top (in the raws)
AoT: ErenLevi - Levi is born an Alpha, but due to trauma in his childhood he suffers from impotency, he worries if he will be able to be proper lover for his mate. However, when his Beta mate Eren turns out to be an omega, what can they do against their biological fate?
Shingeki no Kyojin dj - Hangyaku Unmei — http://www.mangago.zone/read-manga/shingeki_no_kyojin_dj_hangyaku_unmei/
I know this sounds stupid but, Is there in omegaverse case with an alpha wanted to be topped by his omega???
This question has been bothered me all of sudden because of that fake update please don't scold me ha ha(￣∇￣")