Back in the earlier days of modified XJ's hardly anyone cut the fenders, since the tire clearance problems are at the bottoms of the wheel wells, not at the top. Most were careful of the wheel backspacing so the top of the tire went inside the wheel well, or the tire didn't get close to the top of the wheel well depending on lift and tire size. So, trimming was only at the bottoms, and the stock fender flares could stay in the stock location. Lately (a number of years) it seems the norm is to cut the crap out of the wheel wells right off the bat. In many cases that I've seen it was unnecessary and looks like hell. I see fenders cut up before the tires are even mounted and tested for clearance.
However, I do understand if you're going for a very low ride height it would be necessary to cut.