Molecular evolution has double meanings. First, it means a set of natural phenomena, i.e., changes in genetic materials and its fitness consequences over time mediated by mutation and selection. Second, it also means the branch of science that studies the set of natural phenomena.
A book or a course can be named "Molecular evolution" with no confusion, because people understand that the book or the course is on the science studying that set of natural phenomena. Specifically, the book or the course is on 1) the patterns, regularities, theories and laws derived from the set of natural phenomena, and 2) the methods to understand/recognize such patterns and regularities and to formulate theories and laws.
Similarly, a book or a course can be named "Genes" because people understand that the book or the course is on the science studying genes. However, it would be awkward to use "Genes" to represent the science studying genes.
Using "molecular evolution" to represent both the set of natural phenomena and the science studying that set of natural phenomena causes confusion when one says "The fundamental differences between classical population genetics and molecular evolution…" because it sounds as if one is comparing a branch of science with a set of natural phenomena.
This awkward usage of "molecular evolution" with the double meaning has been voiced by researchers in multiple occasions, but the tradition and convention have been stubborn, contrary to the common perception that evolutionary biologists welcome changes.
There have been two proposals to replace "molecular evolution" as a branch of evolutionary biology:
1) Rename "molecular evolution" to "molecular evolutionary genetics" (which is the title of Master Yoda's 1987 book). It is a bit long but is not unmanageable.
2) Rename "molecular evolution" to Molevolution.
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