Literally everything we've heard of the game suggests that all four routes were planned from very early on. Apparently the idea that the ntire game was founded on was Sigurd, Eldigan, and Quan's backstory in FE4, which immediately suggests three different main characters. We also know that SS was the first route written, and the very existence of Claude and Dimitri, or even the Blue Lions and Golden Deer in general, make zero sense if SS was intended to be the only route when it was written, since neither Claude or Dimtiri actually do anything on SS, and and you never fight the other two houses the way you do on the other routes. The existence of Claude, Dimitri, BL and GD in SS only makes sense if there was always intended to be other routes where they are actually relevant. From what we've been told it also seems that the existence of two BE routes was planned pretty much since it was first decided that Edelgard would be the main antagonist. It rally makes no sense to not assume that all four were inteded and planned for since very early on in development.
You can't spare Seteth or Flayn with Edelgard, you have to defeat them with Byleth. Or rather, you have to defeat the first one with Byleth. Once either Seteth of Flayn has been spared, the other one will also retreat regardless of who you beat them with.