If the Alpha kids are the same kids created by John in the ectobiology lab, just sent to a different time, they never had to create themselves, right? So would the post-Scratch trolls have also been created in the pre-Scratch troll session, even though Karkat said he did the same ectobiology stuff John did?

No, the pre-scratch trolls were created in the post-scratch trolls’ universe.  The fact that they didn’t do any ectobiological shenanigans was one of the reasons their session was doomed to fail.

~Mod T