Saying 600whp is a safe limit assumes you’re tuned safely, and if you are, 600whp is impossible on factory turbos.
The tunes you’re referring to reach a “safe” threshold not because of the limits of the short block, but because the pressure ratio you’re pushing the stock turbos to takes you right to the knock threshold on pump gas. Run E50 or E85 and that knock threshold will be higher, so you can run more boost and/or timing and make more power.
Once the stock turbos are at their limit they’re pushing mostly hot air and making so much excessive heat at those boost pressures that timing has to be reduced to avoid knock. The tuning companies like Cobb, etc., need to leave a fair amount of power on the table to account for variability between individual motors and infinite environmental factors. This is why you get an even bigger bump going to a custom pro tune like from Goose, the tune is bespoke to your specific truck, fuel, and environment.
If someone made a kit to strap 2 BorgWarner EFR 7163 turbos on a 3.5eb, I bet you could pretty easily hit 600whp with less than 20 psi of boost. At that boost pressure those turbos would barely be working hard, you could keep pushing it until you blew the motor, then you’d really know the true limit of what the 3.5 bottom end can handle.