The reason is simple; Darwin's proposal for evolution is over 150 years old, and the science of evolution has come along way since. Darwin did not know contemporary genetics and biochemistry. Darwin simply proposed the 'Theory of Evolution, and justly predicted that over time the questions he had would answered by science in the future.
Actually Darwin never described the variation in species as random. He simply proposed that natural selection under environmental change selected for the best variation for the survival of the species.
Not even close to Lamrkism, which is universally rejected today as previously defined.
What is called 'natural genetic engeneering or epigenetics' is just a variation of evolution. I do not agree with Shapiro's terminology of using engineering, and he does not offer an adequate explanation beyond the dominante view among 98%+ of all scientists in the sciences realated to evolution. Some of his views hedge on Intelligent Design by 'arguing from ignorance.'
Lamarckian inheritance, also known as
"Neo-Lamarckism" has absolutely nothing to do with the above and is an old extinct theory, and as defined is no longer accepted by any sane scientists today.
See:
Jean-Baptiste Lamarck - Wikipedia