The cooling system is part of it, but Gary has done some extensive comparison, between the 6.9 and the 7.3. One issue with cooling is in the 7.3 there is a cooling passage for the head that has a freeze plug in it on the head, and block. One the 6.9 this passage is open. This is the only difference between the heads, the 6.9 gasket has an opening for this passage the 7.3 doesn't. Many have seen here the 6.9 is much easier to keep cool than a 7.3. I think it was Farmer Frank that just did a transplant in his slantnose from a 6.9 to 7.3 and was asking about temps the first day he drove it. I know several members that have upgraded radiators to help pull heat out of the radiator, and there is where some have settled on the aluminum radiators. The 7.3 is just harder to keep cool, guys have been battling this since they started to "turn them up". I know that Travis struggled with this on the Enterprise, and had more that 1 radiator built, and finally got one that would keep it cool towing up Jellico, to the point he was on the phone with the shop owner when he hit to bottom of the mountain........ It worked, but took a few tries, and it was a huge radiator (Copper).
I even remember a story of a guy that could make any 6.9 run like the wind.... but would not touch a 7.3...... maybe the same issue.