All products registered by EPA are subject to the same registration procedures to determine product safety. Whether an EPA-registered flea and tick product is sold in a veterinarian's office or an over-the-counter retail outlet, all will have undergone the same scientific review, risk assessment, and risk mitigation process. When used according to the label instructions, EPA-approved products from either source are not expected to cause harm to human or pet health, or the environment.
It is also worth noting that the EPA only regulates externally-applied flea and tick products. The Food and Drug Administration regulates products that are taken internally or by injection. Given that the requirements of laws pertaining to pesticides are different than those for medicines, it would be very difficult to make a credible assessment of relative safety for products regulated by the EPA vs FDA. Market size might further complicate the issue, with hundreds of millions of doses of EPA-registered flea and tick products sold every year. We have no data about how many doses of FDA-regulated flea and tick products are sold annually.