Yeah, if you're going for that approach, it surely makes no sense.
It is possible to still go for a Favor prestige, but you need to turn off the Auto gain Favor option for that (Settings -> Automation Menu).
Still, since you gain nothing from doing a Favor prestige (because you gain Favors automatically now), you can concentrate on when to go for a Gift or Blessing Prestige.
I hope this makes sense :D