Will my road bike fit in the racks on a public transit bus now that I have put fenders on it?
Probably fine

I have a bike (Surly LHT) with 700c wheels, wide tires (35mm) and full fenders (I think same model, but next size up).  The local buses have 2 or 3 different types of rack, and it works on all of them. On some of the 3-bike racks it's difficult to get the arm over the tire in the middle rack, but the fender isn't really a problem; usually I can just move it to the front rack if it happens to be one of those busses.  I think this problem might have more to do with maintenance, since with otherwise identical racks some the arm pulls out far enough and some it doesn't.

One caveat: you have a choice between slowly damaging your fender by putting the arm over the fender, or possibly having a slightly less secure grip by putting it at the front tip of the fender.  On mine that bit of fender seems to be fine despite me smashing a bus rack arm on top of it frequently; worst case I could trim that off, since the bit of fender that sticks forward of the fork crown doesn't seem that essential.

Basically, the racks are designed to be able to handle the cruiser and commuter type bikes, and a road bike with fenders is a lot like that for these purposes.  There's a type of rack, but there's definitely some differences, so it's possible your bus bike racks are different somehow.