Yes, Ziost is in the flowchart as a part of SoR, so I've finished it on my smuggler, but I stopped there to get questions answered.
So there is a mechanic that will allow you to get at least your base companions back even if they die or go missing during KotFE or KotET this was my major concern, so thank you.
For the third part, nothing I did prior in the Chapter 1/2/3 RotHC and SoR has any bearing on the story ahead then? And my other alts will still be able to finish their main stories and only my smuggler would be locked out of previous content ( That I've more than likely already completed all the way up to Ziost ) I read that some companions can have different things happen depending upon what you did in the original story is this incorrect?