If you roll the fenders that will give you something like 1/2" more clearance. The flare is still going to stick off the body 2-3 inches right? So you'll be able to fit a tire under there that will only be 2 or 3 inches inside the lip of the flare.

Again, the real purpose of the flares is to fit the widest tire possible. In order to do that you have to cut the fender lips off and remove all the obstruction, then weld the wheel wells shut again. Otherwise the flares are just there for (crappy) looks.

My friend had a Toyota with factory overfenders. They were bolted on. When you took them off, the fenders were different from the stock ones. The lips were cut off and the edges were reinforced. I suspect that you would need to crimp the edges in addition to welding.