Nightfire - What N8Dogg98 and fiveohw are trying to explain is that because superchargers and turbochargers work through different means to compress air, it is inevitable that they require different amounts of energy to create an equivalent boost pressure. They have correctly extended their explanation to state that, for example, a turbocharger @ 7psi will create Z more net RWHP than a supercharger at 7psi because it is more efficient to use the heat of the exhaust as the energy source for the compression rather than the torque of the crankshaft. I think you understand this.
The next logical step I think you are missing is what causes problems for the stock rotating assembly. You seem to be focused on the train of thought RWHP is the ultimate measure of stress on the rotating assembly. While RWHP measurements in apples to apples powertrains can be a useful relative indicator, turbochargers and superchargers change the scenario to apples & oranges and the RWHP measure loses some of its comparability.
Maybe it will help to think back to the basics. Remember that both of these forced induction power adders increase the mass of air entering the cylinder so the computer can add more fuel to create a more potent combustion. As the boost pressure increases, so does the amount fuel injected, and therefore the greater the explosion. When the boost pressure high enough (and therefore the explosion), some part of the stock rotating assembly fails. (the concept is this paragraph is no different for either power adder).
Each individual engine and tune is subject to thousands of variables, but for the average case we can reasonably say that the rotating assembly failure threshold (in terms of combustive power) will be the same from either source of force induction. Working logically backwards, the same level of psi boost by either a turbocharger or supercharge will cause the rotating assembly to fail.
It goes without saying, all Mustang owners who have forced induction on stock bottom ends will likely try to run the highest boost they can without going past the failure threshold.
Now go back to what N8Dogg98 and fiveohw tried to explain. If a supercharged 4.6 and a turbocharged 4.6 are both running the highest safe boost level, the turbocharged Mustang will deliver a higher RWHP, solely because of the higher compressing efficiency from the turbocharger.
Regarding what the manufacturer's recommendations are for their products - I see no incentive for them to make claims that the stock rotating assembly can handle high boost (or power levels).
1) If they sell direct to self installers and the self installers suffer destroyed rotating assemblies because they tried to run it close to the manufacturer's (high) ceiling, the self installers are likely to not give their products good reviews by word of mouth or otherwise.
2) If they sell through speed shops, they are unlikely to see continued orders from the shops if their kits keep destroying the speed shops' customers' rotating assemblies. Instead, by keeping the recommended boost (power) levels low, the manufacturer is helping out the speedshop by inducing the customer to buy an upgraded rotating assembly from the speedshop. The manufactures rely on the speedshops to stay in business, so it only makes sense to help them especially when that help comes at no cost.
Rather than looking at manufacturer websites for insight to the theoretical limits that each form of forced induction, stock rotating assembly, a 4.6 can handle, instead look to what owners with experience say about the limits they reached. It is generally consistent across many message boards that the turbo 4.6 Mustangs consider their RWHP threshold in the 500s on a stock rotating assembly while the supercharged 4.6 Mustangs consider it in the 400s.
When you throw Nitrous into the equation - forget what I said about apples and oranges and start thinking apples and coconuts. Too many dynamic variables (delivery method, duration, heat, tuning variables, etc.) with Nitrous to keep anyone from making accurate generalizations linking a RWHP level to a level of safety. Maybe there are some nitrous experts that can chime in. But as for me, I know enough about Nitrous to know that it’s very complicated, and I can't help any further.
*edit - fix the autocorrect Stangnet made to fiveoh's name
