I'm thinking he's Becka's father, too (but child custody didn't cross my mind…good theory, Silva). However, if I recall the circumstances of Charon's pregnancy correctly, I figured it was the result of some cult or EoD equivalent. It would explain the 9-month disappearance and getting pregnant from someone other than her high school sweetheart, two things that, as I understand it, were quite uncharacteristic for the young girl.
So, for my theory to work, this other sect would have to have planned for Gage to impregnate Charon for one reason or another, rather than Jack. Maybe their unspoken plans (or Jack's, at least, like he said in the first pages of the first issue) to wait wasn't good enough; these folk wanted/needed Charon with child at 15, no later. Gage, being what appears to have been a challenger for the young MacKay's affections, didn't have the moral standards or romantic inclinations Jackson did, so jumped at the chance, despite being requested to do so from ominous mystery folk.
It's also entirely possible that she got pregnant by either rape or intoxicated consent (which probably isn't consent at all), and in the 9 months it took her to return home, she experienced things so traumatic, that she blocked it out mentally (or perhaps the chrysallis did?). But that theory, I'm sure, has it's own holes.
And speaking of holes…I know of at least one guy from high school who I'm reminded of by Gage. A bit of charisma masking a massive ego, thinking less of anyone around them because they're certain they can get laid quickest, and pretending consequences don't exist. And no matter how much apathy you show, they'll still do their damnedest to try and rub it in your face.
Kids are so stupid.