Names fade in and out of popularity, not always for an obvious reason. As a given name for males,
Allison would have been the surname, probably used as a fn for family reasons (a distinguished ancestor, the mother's birth surname etc). As a given name for females,
Alison is a medieval French diminutive of
Alice, consistently used in Scotland which traditionally had strong links with
France. For whatever reason, then,
Alison became popular in the rest of the English-speaking world as well. This would have two effects: people would be less likely to give their sons a name now perceived as female, and
Allison would be used for girls as a less common variation of
Alison. So it seems that the rise of
Alison had little to do with the sporadic use of
Allison (m). Now, things could perhaps be different because of the fashion for using surnames as given names for both boys and girls, but I think Alison/Allison are well enough established as forms of the same (female) name; like
Ann and
Anne.