Okay, but let’s make your toy model a little more realistic. Instead of 100 preferred insertion spots, start with 100 million preferred spots. Now insert 200,000 ERVs over those 100 million years, independently and randomly in the two species. How many of the 200,000 will be in the same place?
Now make it even more realistic. The viruses that insert 100 million years ago are now from a different family than the viruses that insert 95 million years ago, which are different from those 90 million years ago, and so on.
What you will get in this model looks nothing at all like real ERVs.