The two V-6 SHO engines (3.0L and 3.2L) have the same overall timing belt path length (hence they can both use the same belt), but the 3.2L engine was developed after the 3.0L engine and was equipped with a belt vibration reducing idler pulley on the forward, tension side of the belt. This forward idler pulley increased the belt length required between the front bank intake camshaft index mark and the crankshaft damper index mark by one tooth.
It also reduced the maximum span and resulting vibration amplitude of the belt span. Along with the gas piston tensioner that applies constant tension over the life of the belt, this new belt path design allowed Ford (Yamaha) to extend the timing belt replacement interval from 60,000 to 100,000 miles.
If the fixed idler pulley is used on the forward, tension side of the belt, the "3.2L" alignment mark should be set at the crank damper's index mark. If the 3.0L's long, undamped tension side of the belt routes from the crank damper directly to the front bank timing belt pulley, the "3.0L" alignment line should be set with the crank damper's index mark.
P.S. SHO folks, I'm around, but I have been traveling a great deal. Only one more trip to Reno, NV, next week (Dec 5-10) and then I am off work and home for the holidays.