to take the extreme case in the simplest form, the stress on the crank at 800 hp at 6000 rpms is much more than 350 hp at 7000 rpms. Not that anyone makes 800 hp on a stock bottom end at the factory rev limit
As a thought experiment: Mass times velocity equals the stress on the crank. Stock power for 99-04 engines is 260 @ 5250 rpms. That's obviously pretty damn close to 260 torque at 5250 rpms. Torque is the measure of the twisting force on the wheels, and so a measure of the twisting force on the crank as well. The twisting force on the crank is what we are concerned about.
If the stress on the rods and pistons (and therefore the crank) at stock power levels is = 1, then at 5250 rpms we have 1 x 5250 = 5250 for a "stress level." Increase the power to say, 400 torque/HP as it is widely accepted as the max "safe" level with a good tune on a supercharger, and we have a new stress level of ~1.5 x 5250 = 7875. Commonly considered safe and reliable with a "safe" tune - i.e. no detonation.
300 torque at 7000 rpms also gives you ~400 hp, and since we got there mostly by increasing rpms rather than greatly increasing cylinder pressures, we are not greatly increasing the stress on the rotating elements vs. supercharging. Going by our above math we get ~1.15 x 7000 = 8050. A marginal increase in stress over a supercharger. Given the much lower risk of detonation due to the high rpm, we actually *could* have a safer build.
Considering the fact that one isn't going to get 300 pound-feet of torque on an NA stock bottom-end 4.6 at a godly 7000 rpms, I think it's safe to say that as fast as you can spin it, the stock 2V bottom end is fine naturally aspirated. If you make 350 hp at 7000 rpms, you are only making ~260 torque at that rpm, and so we get 1 x 7000 = 7000, which is safer than making 400 hp with a supercharger and a stock rev limit. Strictly going by the numbers.
Considering that the 05+ 4.6's use the same crank and rods and the "Track pack" is a dealer-installed option that includes bumping the fuel cut-off up a few hundred rpm based on simple intake pipe/catback mods, I'd say that the engineers at Ford have tested the thing to expiration and are comfortable as you on your couch that the stock 4.6 2V/3V internals are stronger than they need to be.
But if it were me, I'd have the crank balanced when I replaced the rods and pistons so I wasn't relying on a factory external balancer to balance aftermarket guts - regardless of which crank I went with. But maybe that's just me.
In all this keep in mind that there is *theoretically* no difference between theory and practice
And I like doing the math and logic, but both may be wrong.