The specific Berkanan lvl 15 guideline (HM p.129 upper box) says "Ensure that the target is potent or fertile for the duration." (Bolding mine)
I read this as: if she can be fertile at all, she will be at that time. Otherwise that HM guideline were not aligned with the ArM5 CrCo guidelines.
The bothersome side effect of the LR is not meant to be waived with a simple application of magic - Hermetic or not. So the defensive troupe puts effects like the permanent sterility caused by a LR into "essential nature" (ArM5 p.79f). Aurulentus (MoH p.15ff) needs to make his Minor Breakthrough, after all.
The second part of your argument doesn't make sense at all. If a magus is sterilized by a longevity ritual, and the sterility were thenceforth considered a part of his Essential Nature, then that itself would violate the Limit of Essential Nature.
Think if it this way- the longevity potion redirects the creative force of procreation into maintaining the maga's youth and extended life.
You can't have it both ways, at least not without a massive breakthrough.