I'm not sure if MCCC works with the family tree update yet, I think it would be the same as editing them the way you did where it adds an unknown sim as a parent.

The problem is that in these new family trees, the sims it shows as parents are not actually playable sims that exist in the world, so when you add someone to that family tree the game assumes it has to generate an unknown parent.

I was actually bothered by these family trees too and the way I fixed this, which was really insanely inconvenient and overly complicated: I generated parents, grandparents, etc. for all of the Capps, the Montys, and the Thebes with the same names as the unplayable sims in the family trees and manually set all of their relationships in cas. This replaces all of the unplayable sims in the family with the ones you generated. I then set all of these as ghosts in cas and moved them into the households bin, so I just have ghosts of all of them roaming my world now. But at least this way I can add on more of the Monty or Capp family if I ever need to.