A simple explanations: the genetic difference that regulates the biological clock is tiny, which makes variations common, because on the perspective of millions of years such variance is useful, as it increases adaptability and thereby surviveability of the species.

Massive increase in hunters during the day? Small mammal ancestor of humanity becomes a creature of the night within few generations. Sudden ice age, night activity is energy expensive, so curl up, sleep, and search food during day is the best strategy? Adapting quickly to such changes is a benefit. To get that benefit the mutation must be common.