The first question would be to ask why this would result in ERVs that look like they evolved at many different levels of evidence, such as species distribution and LTR divergence. For example:
Why would a designer need to give humans an ERV at a specific position in their genome if that ERV is found at the same position between chimps and orangutans?
If a specific family of ERVs is found in the chimp and gorilla genomes but not in the human genome, why would a designer be forced to put the ERVs for that retrovirus family at different locations in the chimp and gorilla genomes?
Why would there be more divergence in the LTRs of a specific ERV if it is shared by many primate species than if it is shared by just two similar primate species?
Common ancestry and evolution explains all of these patterns of divergence and shared ERVs. If “original design” can not also explain these patterns then it isn’t a valid scientific explanation. On the flip side, could God create species so that they look like they evolved for no other purpose than to fool us? I suppose, but that doesn’t seem like a road that most theists want to go down. Therefore, if the evidence is consistent with evolutionary mechanisms and common ancestry and “design” can’t explain these patterns, then design is not the best explanation.