It does matter alot
Assuming you are shooting in an indoor environment.
scenerio 1. Your setting is at f4 and 1/60secs and iso 200, you look into the viewfinder and find the exposure meter showing that you 3 stop underexposed (assuming centre weighted). With your flash at iTTL you released the shutter and flash fired. What do you think is the power of the flash output?
scenerio 2. All the same setting and location and subject, but now at iso 1600, you look into the veiwfinder - what would be the exposure meter showing you? and when you release the shutter and flash fired, would the power of the flash output be more? or last than the first scenerio?
If you can answer it than you will now know whether it matters.
Anyway why at iso 200 in indoor ? The D3 is one camera where at ISO 3200 is still very good to print up to S8R or more. That's one of the strongest point of D3.