I get that the developers were fine with it the way it was, but in the interest of continuity and the story making sense, it probably would be a good idea to remove the ability to absorb Lord Kemm, Isbeil, and Sallow Man's souls or remove them from the final fight if they were absorbed and put in non-unique summoned NPCs instead.
Also, it's not like making Kemm, Isbeil, and Sallow Man unable to be devoured would take much effort as the code is already there from what happens when you try to absorb Windego after the 2nd fight with her. That code could very easily be modified and applied to the other three NPCs I mentioned and that would solve the problem completely. They'd be there because the God King took their souls, which would make a lot more sense than the player absorbing their souls and they're still in the final fight.
Heck, even the DOS2 Wiki (link:
https://divinityoriginalsin2.wiki.fextralife.com/End+Times ) says that Lord Kemm, Isbeil, and Sallow Man shouldn't be there if they were absorbed and that the Kraken would summon no-named NPCs instead, like Black Ring Painreavers and Fearmaidens, etc. So not even the wiki is accurate.