You haven't read it. He titled a whole chapter "On the Limitations of the Geologic Record." His conclusion is that we have crudely the geologic record we would expect given his model of evolution and the reigning model of geology. IOW, you are flat misstating what he actually had to say on the subject.
And I bet the rest of your supposed information is of a piece. Care to state the mechansim of evolution for us?
Working from memory. As everyone must realize by now--curse PH and his links!--it's "On the Imperfection of the Geological Record."
As a matter of fact I have read it, and more. I would gladly state the mechanism of evolution for you, if I believed such a mechanism existed.
I believe that the Bible is a key to understanding how things come into existence, but not in the sense of a hoary thunderer creating the earth and its creatures in seven literal days. I believe that the key is the text of the Bible itself. Opening the book of Genesis to the first line: "Bereshit bara elohim ET", ET is an acronym (as are many words in the Hebrew language) that is a marker meaning "a definite and direct object comes next". It has however, a deeper meaning. The word ET is spelled Aleph-Tav, the first and last letters in the Hebrew alphabet, and is also an acronym for the alphabet. The first line literally says "In a beginning, God created the alphabet."
Exploring further one finds that the whole of the Torah is a coded explanation of hyperdimensional physics in base 3. (Trinity) I could go on for hours and pages explaning the "missing link" that is there for all to see between consiousness, language and creation, but being the inveterate capitalist that I am, you're going to have to wait 'till the book is published. Suffice it to say that John was being quite literal when he said "...and the WORD was God. He was with God in the Beginning. Through HIM all things came into being..." (The "word " used by John in the Vulgate is "LOGOS", which means not only the word, but the spirit that causes the word to be.)
Consiousnes preceeds the form we take. It is not the result of it.
(By the way, didn't Archaeopteryx have its own distinct DNA?)
Best wishes to all seekers of truth, whatever their persuasion.