That is an excellent question.
If one assumes that the process works as you say, then one would expect to find that particular infection events would occur in the target species with a random frequency unrelated to the presumed common ancestry of various species. Humans, for example, just by chance, might be missing an infection marker which exists in other higher primates.
But that is evidently not what is found. The infection markers demonstrate a non-random frequency which suggests the same common ancestry as other evolutionary evidence.
No, I'm suggesting the possibility of an enzymatic mechanism for the insertion locations as opposed to nonfunctional products of retroviral infection that have inserted randomly into the host. The whole proof of the common descent explanation lies in the vast improbability of mostly random viral insertions occurring in the same location in two different mammalian species because the DNA chain is too long for coincidence.
Cordially,