That's a great question. I've been considering the same dilemma for a few years. Here a few more thoughts for you:
1) the metal mesh of the roof rack itself will make a good ground plane. Are you planning to mount your NMO to the rack, or to the sheet metal of the roof? I'm thinking the rack is the best option, since it's the highest possible ground plane. As you said, mounting to the sheet metal leaves the possibility of the rack changing your radiation pattern.
2) Assuming you're mounting to the rack, what will you do when you want to take off the rack?
3) What are you carrying on the rack? Bikes, tools, metal gas cans? Any of those things will change your radiation pattern, at least a little bit. Your signal will still get out, but does it negate the advantage of having a roof mount antenna?
Because I couldn't answer 2, and 3, I compromised and mounted my 5/8 wave to my fender :/ I'm interested in hearing how others answer your question. Maybe it is time for me to move my antenna to the roof rack!
Motorized expo: 2000 4Runner SR5 4x4
Non Motorized expo: Serotta Coeur d'Acier, Surly Cross Check, IF Steel Delux, Surly 1x1, LaPierre X-Lite