I'm with Drew on this. In design terms there's what's called the "form vocabulary". Referring to cars and trucks, form vocabulary would be the various design elemnts that stick with the manufacturer's designs from year to year. BMW for insatnce, uses the split kidney grill design. They've evolved it year after year, but it is still persistent and says BMW whnever you see a car from them. Mercedes, Jag and Jeep grills, Porsche front ends and shape, Dodge trucks grill and fenders, Mustangs, Volvos all have a number of form vocabulary design elements that you recognize and visually use to define what that marque "looks" like.
On the FJ's, the grill, white top, box sides, and round headlights all say "FJ". Notice that the new FJ Toyota is working on carries those design elements forward albeit it un updated style. Like the Mini, and the new Bug, the FJ is an evolution of the original; design form vocabulary.
I don't think are many vehicles from Toyota which have manitained a classic sense of form vocabulary, but the FJ was one of them. I'd say the white roof iis a part of the look of the FJ that you should mainatin if having the vehicle look like it was intended to is important. If not, go for the body color of whatever color...
One other note- spraying the big white roof panel is a bit of a bear. It's really wide and tall, hard to get over without dragging your air hose over your work, and for this old guy, seeing the paint from pass to pass on the 2nd and 3rd coats was damn hard with the white, my eyes had trouble staying focused. White is a tough color to shoot.
