Casual reminder that this is still the case and is still not fixed or, as a matter of fact, even mentioned in any dev posts as far as i can tell.

If we're talking about Ossus, there are several blasts from the pasts, though i don't recommend starting it if you chose Darth Zash over Khem Val back in the latter's final quest - there is a bug they still didn't fix. Pervious story lines have more about you & Alliance rather than anything else, but there are some missions where you can gain certain position in regard to the Empire, though you will still remain independent power regardless.

So wife of the former Sith Emperor.

Noname as in "former Sith Emperor who literally consumed all Force from two planets" or as in "son of the former Sith Emperor"? But yes, without spoilering, Commander becomes pretty important and Alliance becomes pretty powerful at the end. At that point seat in the Dark Council would be merely a downgrade.

Same here. Played Nathema Conspiracy only two days ago and game recognized this choice corrrectly back then.

Same here. Played Nathema with this character only two days ago, Khem correctly joined Order of Zildrog's operation. Now encountered him during Ossus mission where you locate stealth supply drop (don't remember the name), immidiatelly ESC-ed from dialogue and reset the mission. Can provide more detail about character status if needed.