This has been identified at least once before. See here. The folders named Icons and Images are not replaced. There may be others?
Personally I have no wish to preserve these folders on a restore and would prefer the Replace existing configuration completely option to do exactly what it says. Maybe there is case to be made for a Replace existing configuration except for personal folders option to be added for those who do want to preserve icons and images?
I don't think it makes sense, so we'll be changing it. (When looking into this, I found I had accumulated a folder of unused iconsets myself due to the same thing.)