At least pre-reboot, while Booster was Rip's father, Rip's mother was in fact changing.
Note that Rip's appearance changes between 52 and the Booster Gold series. In fact, one villain even notices it. This is because that while Booster is Rip's father, the identity of Rip's mother keeps changing as Rip affects Booster's life. No matter who Booster eventually hooks up with, that first child will be Rip, but until that becomes "solidified time", half of Rip's genome is in flux.
Hence why Superman and Wonder Woman kissing has removed him from history.
A different relationship of their main reporter Clark Kent than one with Booster's timeline is going to result in radically altered histories, and if Booster is descended from one of them, the 400+ years of the ripple effect would escalate to him never having been born.
- This actually proven to be the case for Superboy.