Well,Ford using the 8.8 rear end instead of the 7.5 they have always used in the V6 leads me to believe they were thinking about drive train upgrade at some point.
Anyway I look at it the driveshaft in the 3.7 is inferior.
A lot of the heat in this discussion stems from a couple of your assumptions. Ford using an 8.8 rear end in the V6 doesn't mean they intended to have V6 owners to start using 3.73 and 4.10 gears in the back of the V6. Streamlining parts across multiple platforms brings a lot of operational efficiencies to the table vs having them use different rear ends, transmissions, brakes etc.
I'm fairly confident Ford didn't intend to have v6 owners swapping to 3.73's and removing the speed limiters. I think they had concerns over the driveshaft beyond 115 mph with a 3.31 rear end. How this applies to other people who've encountered failures below 100 mph I have no idea. I think we can all agree that we're only guessing vs stating the facts.
I personally wouldn't do gears without the driveshaft but I probably wouldn't criticize them for giving it a go either. I also don't believe Ford owes anyone a driveshaft. They made a pretty deliberate attempt to avoid having anyone reach the critical speed of the driveshaft with the speed limiter. The issue from the start was most people including me assumed the speed limiter was there for the base 17" tires while we questioned why they didn't remove it for the Performance Package.
See how those assumptions work?