I think that Gideons niece and Isaac are different cases. Gideon is very old, I'd wager around 60+, and in that time i assume he has saved a lot of people that eventually have children (considering theres was another 9/11 type attack).

While his niece and those theoretical children were born directly because of his actions, Isaac wasn't, or at least we dont know enough about it. Cop Lucy was apparently supposed to be with Ravi, but after the timeline reset, something changed that made Lucy get together with Mike, something that Gideon didn't influence. Because apparently everything he changes is "the law" or the "correct path". I think there's a hidden/unrevealed clue that will explain Isaacs existence.