Yours stick out because you have aftermarket wheels...do you know the backset on those? Probably 3.75" or so...the stock wheels have an inch or two additional backset. This will also affect how/where they rub. On stock wheels they are more likely to rub the inner side of the fender at full turn, more so than along the wheel lip.

It is true that the 10.5" wide 33s will be less likely to rub - but plenty of people with only an OME lift have run 285/75s with little or no rubbing on stock wheels, and they are about 11.5" wide IIRC. With 3" lift he should be in pretty good shape...if somebody has direct experience with this particular configuration (2nd gen Trooper, 33" tires on stock wheels, 3" suspension lift) chime in.