That's a good question. I tend to think it makes a lot of difference. Assuming that by "comfort" you mean the extent to which a tire will absorb rather than transmit minor bumps in the road, there is no question that at the same volume and pressure a more supple tire will be more comfortable. But as you change more variables, things get complicated. A really wide tire at really low pressure will likely be more comfortable than a really skinny tire at really high pressure even if the wide tire is less supple. But the comparison you asked about involves small changes in width and presumably small changes in pressure.

I suspect that in the real world most people (myself included) would have a tendency to overinflate the 28mm tire (because their mental model of it is as a race tire) and that the 32mm Gatorskin would on average be more comfortable. But if you used some mythical ideal inflation for both tires, I think the supple casing of the GP 4000S would give it a slight edge.

I could be wrong though. Air volume goes up pretty fast as tire width increases.

FWIW, I've got 700x28 GP4000S's on one of my bikes and they measure closer to 30mm wide. I don't know about the 700x32 Gatorskins. Also note that the more supple GP4000S's will have less rolling resistance and on relatively smooth surfaces your brain may very well interpret that as comfort.