If you are going to use medium-to-fat tires on a bike all the time, then you should really consider switching out normal-width rims for wider "downhill"-style rims.
Fat tires work best on w-i-d-e rims. You can drop the inflation pressures lower, while still retaining good handling qualities.
Also rocks rolling under the fenders: yea, I've heard of that.
I looked a long time for plastic fenders that would fit around BA's while still leaving decent room, but still fit into a normal bicycle frame,,,,,, and didn't find any. The problem is not the tire's width, but the tire's centerline outer diameter. It comes very close to rubbing at the front and back edge of most every fender out there.