I am going to make a couple of assumptions here. Since Uke is normally the "passive" partner in the relationship, it would stand to reason that they are the younger in the couple, while the Seme, being the dominant partner, is the older one.
In a school scenario, senpai would make sense and I'd assume the Uke would start calling the Seme by their name (probably with the -sama honorific at first) when their relationship is a bit more intimate (intimate = anything after their first kiss).
While I don't read Yaoi, one can't assume that every Yaoi story has the Uke and Seme attending the same school. There may be some where one attends a different school or doesn't attended at all, as such senpai could still be used.
However, the Seme, being the senior, is still guiding the Uke like how one's senpai guides, protects, and teaches their kōhai as best they can. With that, senpai becomes a term of endearment from the Uke after having been guided in the relationship by the Seme.