Hey J.: There is a ton of dye and preservatives in mac & cheese... So it might be a reaction to ingredients besides milk. My DD has a confirmed allergy to cow's milk and my dear, dear husband decided he should reconfirm it himself and let her eat cheese... which resulted a huge red diaper rash which made her cry when she pee'd (Thanks honey!). Your description of his rash reminded me of my daughter's reaction to when she ate that cheese.
Since he is ok with drinking milk, perhaps your son has an allergic reaction to certain cheeses more than others... Or the curding enzymes? or the dye? Perhaps he is having a reaction to the mold that makes cheddar...? Was the cheese he ate a processed cheese or an aged cheese? I have one friend who told me that her son reacts to processed cheese differently than regular cheese... My suggestion is to stay on BRAT until better, then hold off cheese and yogurt... introduce plain noodles and plain tortia (to test for a flour/gluten reaction), then introduce meat (since that was part of the meal he reacted to), then introduce yogurt (to confirm no milk allergy) and lastly introduce cheese and see if he has a reaction. And of course, throw out the butter/milk that you used to make the mac & cheese in case it was slightly turning and he is simply reacting to that.