Possibly unrelated and in the same game save as posted above, cannot create a commonwealth, "Missing Data" name your new faction etc messages and no matter how many times I try to name it, it keeps popping the dialog.
I have one with Drath, I mentioned it in discord but can't post there due to file size As I also said in discord something that may or may not be related, I got the Commander tech through a trade prior to being able to research it, ie I didn't have the tech directly preceding it in the tech tree but got it caught up later. You can see in the game save it has the same "no room" tip hovering over the disabled assign commander button. https://ufil
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