Can goat's milk be used to cook sheep's flesh? The species are different — goats and sheep — but both are domesticated livestock. The Mekhilta extends the prohibition through yet another a fortiori argument, this time drawing on the laws of mating animals.
In the realm of reviah (animal mating), the Torah permits "fruit with mother" in cooking — meaning the original verse addresses only cooking a kid in its own mother's milk, not cross-species combinations. But the same Torah forbids cross-species mating — you may not mate a goat with a sheep ("fruit with fruit" of different species).
Now apply the logic. If in the realm of mating, where same-species parent-offspring combinations in cooking are merely the starting point of the prohibition, cross-species combinations in mating are also forbidden — then in the realm of cooking, where even same-species combinations are forbidden, cross-species combinations must certainly be forbidden too.
The Mekhilta systematically closes every potential loophole. Same species, same animal? Forbidden. Same species, different animal? Forbidden. Different species entirely? Also forbidden. The a fortiori chain extends the prohibition from its narrowest Torah formulation — a kid in its mother's milk — to encompass every possible combination of meat and milk from any kosher domesticated animal. What began as a single specific prohibition has been expanded through rigorous logic into a comprehensive dietary law.