Thanks for the reply.
The optometrist was reasonably confident I don't have KC, and the Topography test the AME did was normal too. But with the fact I have Crohns and the potential deterioration of my eyesight, he thinks it's worth the referral.
I'm very interested in going down the Class 2, to Class 1 route. I did infact ask the AME doctor about having a Class 2 for now, which I'd use with gaining my PPL. But he recommended appealing to the CAA in regard to gaining my Class 1 first.