The "dream" of Zanarkand is basically a whole frickin' pantheon of Aeons.[1] Seeing as Aeons seem "alive" in that sense (they have physical bodies that can be hit and incapacitated, even killed) it makes sense to me that they'd be capable of breeding to a certain extent; just means the Fayth have one more Aeon to upkeep. It's ever so slightly like the Matrix, only this time it's not necessarily one body per mind or vice versa .

Bit of a simplification but that's the easiest way to see it.

[1] Something like "They all became Fayth. Fayth for the Summoning."