Is it true that the main reason for the preset doom of Kankri's session was because they were not born in the game through ectobiology? And if true, then what happened to the '12 extra grubs' Karkat made?

One of the reasons they needed to scratch was because they were made post-scratch. They are the 12 extra wrigglers that Karkat made. If the pre-scratch trolls didn’t scratch then they couldn’t exist.