That's not the base Z. 6.9 million yen is for the Proto Spec, aka limited edition like with the 2020 LE. The base Z will be around $40k.
https://www.nissanzclub.com/forum/threads/jdm-nissan-fairlady-z-photos-spec-and-press-release.757/
It was 20% for the 2021, but it now has been cut down to 15% for the 2022 model. Production or take rate, whatever, point is only 15% is available this model year...
The math still doesn't add up. For 2021, the 2.0 has an take rate of 15% while the 3.0 makes up the remaining 85%. Toyota themselves stated that they predicted that 30% of buyers would opt for a manual.
MT with 30% applied
2.0 = 4.5%
3.0 = 25.5%