On definition of evolution:
Darwin's book does not concern itself with the origin of life. In fact, it merely suggests that God created the first form or forms, and leaves it at that. It is
entirely about development of existing life, and does not address abiogenesis at all.
Your telling phrase is "at least from the atheistic viewpoint". Your point (however good or bad it may be) is
contra atheism, not
contra evolution. Actually, I'm a theist but I do strongly suspect God used natural processes for the origins of life.
No, "seperation" of chemical and biological evolution is not a new development. They have always been quite seperate.
On reptile/mammal transitionals:
Since the transition took of the order of 100 million years or so, from the late Carboniferous through to the early Triassic, why should various forms not radiate, as later mammals have done? Would it make sense for them to say "hey guys, let's hang around here until we've fully evolved into mammals"? Not sensible. Geographical considerations aside, you still have to deal with the sequence, and the remarkable congruence between the transitional state of each specimen and its age. Unless you suggest we consciously fiddled the figures?
And I have no idea what
Moreover, intercontinental correlations are made even when the fossil genera do not correspond with each other. means.
On Transitionals
Most disputes are not about whether a specimen is transitional, but exactly what the transition is. No-one within mainstream science disputes that
Ambulocetus is transitional, but debate rages over what the exact ancestor of it was, and what course evolution took between it and modern cetaceans, or whether Amb. is truly ancestral to modern cetaceans, or merely a cousin. None of it helps creationism in the slightest, because
Ambulocetus shouldn't exist at all for you!