Although the Epilogue Quest line does allow your faction to leave the planet, in ES2, it seems that only the Vaulters and Sisters of Mercy (as far as we know) made it off the planet alive (via the Argosy). This is described in the Vaulters Questline as well as shown in both the Vaulters Prologue and the Amplified Reality Trailer. The Grey Owl (this Hissho starship that takes your faction off the planet) is blown up in a Dust explosion that many of us theorized (really early on) was caused by the "narrator" of the trailer (either Isyander or a Lost individual, I can't remember who). This dust explosion also happens to be the same one that causes a dimensional rift in the Cortoz and forces the Riftborn to enter the Endless universe. 

So basically, no matter what faction "wins" the EL campaign, canonically, only the Vaulters and Sisters of Mercy survive. Although it is possible that in the future Amplitude will show that other factions survived with the Vaulters/Sisters of Mercy in the interior of the planet, and used Endless Tech to leave.