He suggests that it wasn't literally every ship in Starfleet that had its own badge, just different subsections of it. When Earth, Vulcan, Tellar, Alpha Centauri and Andor formed the Federation, each world contributed its ships to a portion of Starfleet, with different missions for each subsection of the new fleet.
Here is a picture describing all of this.
In his view, it was just a coincidence that every ship we saw had a different emblem, since they came from the aforementioned divisions of Starfleet. And of course not every ship within any given division had a crew comprised only of one species (the
Intrepid did, but not all).
I asked him once about the
Defiant badge, and apparently he believed that it was similar enough to the
Enterprise one (just pointed in a different direction) that it wasn't worth worrying about.