[nissanfanatic]

The only thing you are really combating when it comes to high CRs and high boost is heat. You combat it by retarding timing, running higher octane fuel, and anti-knock.

Typically longer stroke equates to more torque. But with more boost on the short stroke setup, there is no reason you can't make equal torque. The plus side to the shorter stroke is higher RPM AKA higher horsepower with supporting mods.
What you described, running lower CR pistons with longer stroke or running higher CR pistons with shorter stroke would depend on the setup. Esp cam timing, port size and amount of boost. But yes, peak torque would be regained when you hit full boost. Peak torque occurs at Peak Cylinder Pressure. So as long as PCP on one setup is higher at one point than any other on the opposing setup, you will make more peak torque.

Personally, I would take the short stroke+Higher CR engine just for a longer powerband/smoother powerband. Assuming I had the money to build to my preference.lol