IMO the transmission argument boils down to the mission statement of the car.
A GT-R, or crazy modded Supra, or Lambo, or GT2, or Ferrari, or (insert crazy 500+ hp weapon here) are technical marvels aimed at laying down maximum performance on a track. Makes sense to have a transmission matched to the performance level. Otherwise...why exactly are you purchasing that performance level?
The 3 pedal argument is for driver engagement (loosely defined) over outright track times. Cars like a 911, 911S, S2000, mustang/camaro, miata, cayman, and the compact sport sedan class (though only BMW offers one) would seem to fit here.
All of the latter group would be very fun track weapons for 99.99999% of car enthusiasts. And if, as they claim, they care about engagement over outright performance, then they'd be perfectly happy to "just" drive a 911 S (and not some bonkers GT2 missile). Regardless of budget. But that's the rub. There are rich guys who also like manuals and can't stomach driving such a lowly porsche. And so you see creations like the 911 R and the return of a manual to the GT3. Whether it actually makes sense is another question...
I applaud GM for offering so many manuals, but will admit it is somewhat curious in a car like the Z06. Surely a manual-enthusiast would be content with a Grand Sport and leave the outright maximum performance chasers with their auto Z06 option.
I'd always want the 3 pedal option, but also wouldn't be expecting it to be paired with a 600 hp drivetrain. Makes no sense.