I use a PAT bus every morning and always put the bike-retaining arm over the top of my front fender. I’ve never had a problem with the bike coming loose while in transit. Just make sure the bike is fully seated in the rack and pull the arm over the front wheel.
One problem I did have once was when the arm hit my brake pad and knocked it out of alignment. Fixing that was 30 seconds of my life I’ll likely never get back. sigh.
To ensure a proper and safe loading, the bike rack support arm must be as close as possible to the bicycle’s head tube. Most fenders will flex under the support arm and be fine, but some types of fenders may not withstand the pressure of the arm. Cyclists are encouraged to check with their local bike shop for fenders made from a material that is robust enough to hold up under pressure.