I have the bumper-mounted lights, and IMHO, they are more prcatical for everyday use. You can use them on road if you need to, wheras you can only use the roof-mounted ones off-road.
I would be remiss in not adding that I hardly ever go off-roading, so I do not need the roof lights, plus I can't add anything to my FJ's roof anyway, even the stock roof rack, as it would no longer fit in our garage if I did so. (The top and sides of our garage are brick.) But, even if I could, I still would leave my roof "bare", so to speak.
Best of luck in deciding and post up some pics when you get your new FJ!

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Sun Fusion 4X4 AT CQ GY DL FE XY PW CA TC QS
Mods to date: New and Improved Tire cover, with the FJ, tire tracks, and the word "Cruiser" free-hand painted by my wonderful wife
A-Trac,Dual horn,Goodyear Fortera Silent Armor's w/MB Razor wheels
Florida "Shark" specialty license plate saying "KRUSR"