In the classic yaoi world smaller male meant uke, they were supposed to be cuter than the seme and less dominate in every way.
Seme however were supposed to be the apex male, thus larger and more manly in everyway.
Plus the sex scenes are just much more erotic if the seme has a giant sick. It would not be so sexy if it was the other way around. In yaoi mangas, old or new you see the uke often comment about the size of the seme during sex or during foreplay scenes, it's allows the mangaka to create pillow talk to arose the readers.
And this is just another opinion but i think many people fantasize about taking large dicks (I'm guilty) or see it as super hot, so the mangaka play off that fantasy. But ultimately it just makes the seme look better and more dominate than the uke.
sexism
Why is uke's dick always smaller than seme's?