François,
If I understand correctly your problem, why not simply use a regex search when editing your epub?
Of course, you have to do it for each epub, but it's just a matter of saving the regex.
By the way if you are using "vertical-align:top" for, let's say Mme or 1er, the following code is working adequatly, at least with my Kobo Touch :
Code:
sup {
font-size: .55em;
vertical-align: .60em;
line-height: 0.5em;
}
Of course, this code can be changed as needed.