Hmm, I'm not sure what might cause that, the logic for classic mode is pretty straightforward where it just auto-flags the CCS as having already been defeated at the start of the game. Can you post your save so I can see if there's anything weird in it?
I don't have any specific plans to add more modes, although Democrat/Marathon mode aren't that difficult since all they do is modify the victory condition. I'm not sure what extended endgame is, I don't think that was a thing in the version I based mine off of