The sleight of hand here resides in the words "the process thereafter". The evolution of existing populations by natural selection (and/or by other means) is not the same process (or even the same kind of process) as the chemical events by which the first replicating cells arose. We have as yet only a sketchy understanding of the latter, but that puts no constraints on our understanding of the former.
For the most part we have very little idea how a language's grammatical rules came into being; that does not stop us understanding the language.
I disagree with your analogy. The TOE does try to explain how life developed, much the same way someone may study a languages development. Understanding the behavior of an animal does not mean you understand or know how it got here, anymore than understanding a language gives insight into its origins. The ToE claims to know how life developed but cannot explain its origins. The Bible, however, does explain both origin and process. (Psalm 36:9, Genesis 1)