Is there a broader nomenclature convention to explain why the ‘a’ in ‘chlorophyll a’ is italicized?
This is only a partial answer to your question.

The suffixes a and b to the name chlorophyll were most likely introduced by Richard Willstätter and Arthur Stoll. They are widely used in their book UNTERSUCHUNGEN ÜBER CHLOROPHYLL (Julius Springer, Berlin, 1913). Here, however, the suffixes are not yet italicized and appear as normal text.