I wonder if the experiments could be planned to have the same final parameters. For example, plan to add salts to keep both the mash pH's the same and plan to add enough capped roast malt to make the colors equal. After all you're trying to find out if there's a difference and you've already built in a difference. Knowing that the pH would be low and the color would be light makes the experiment kind of pointless imho.
From what I understand, Gordon's method was not so much to smooth out the flavors, but also to simplify the main mash. If you do one mash and add the proper salts or acids to get the pH you want, then you never would have to measure this stuff again. Just do the main mash then add the crystal and roast malts later. Without any of the excellent water programs used, this makes sense for a beginning all grain brewer.
I tried capping the mash several times and didn't get the colors or flavors I wanted, so I went back to the usual method.