I want to get full fenders.

Sometimes I put my bike on the bus racks. Will the fenders get damaged or will they be OK if I put the clamp thing over the top of them?

Don't suggest clip-ons. I have them already. I ride dirty roads and when it's wet, my bike ends up a big huge mess.

Looking for answers from people with actual experience in this matter.

I don't have an answer for you, but I've wondered the same thing as regards my car bike rack (an earlier version of this one: https://www.thuleracks.com/thule/imag.../thumb/916.jpg). It holds the front wheel in a similar manner to the bus racks I've seen, and I've wondered about possible damage to the fender -- or if I could engage the hook just in front of the fender and still achieve a secure grip on the wheel.

I haven't had any problem with them. They aren't getting deflected that far. I used the hook part under the fenders and over with equal results. I don't like to do it, but sometimes there is no option. Like newsace, my experience is with the consumer version.

If the Yolo bus's racks are like the RT's racks you should be fine.

I've put my bike on the rack with my Freddy Fenders with no problem. I just put the hook over the fenders as close to the mount as possible, and it rode just fine.

I have considered cutting the front fender so that it does not stick out past the head tube. Seems like the main reason for the fend is behind that point.

Actually The front part does keep a lot of muck off of you and your bike. I wish that clip on fenders were just longer, both front and rear.

The one bike that I own that I also use on bus racks has a wide gap between the tire and the fender. The gap is wide enough that I can fit the rack mechanism between the tire and fender. I use Planet Bike Freddy Fenders on that particular bike. They have quite a bit of adjustment for the clearance of the front fender. I set the clearance specifically with bus racks in mind.

Good question I've wondered that myself...I've got SKS commuter fenders on my XO2 and run a rather narrow tire...from past experience I think having clearence would be ideal...they're retro fitting the buses around here with racks(I Can't believe it)...may end up trying to ride one soon as it gets colder...but for now I'll just pedal on...

cycocommute warned me last season about putting the hook over the fender. Apparently, the bus driver had to pull over for him to adjust it. I think it was in danger of falling off.
All bus instructions state to put it under the fender.
I run sks fenders on my touring bike. Everyday I use the bus and have no issues. I simply pull the fender up a little to allow the hook to cover the tire. Fender material is fairly flexible. My old freddy fenders were mounted on my hybrid slightly higher to allow the hook to engage.