The gearing is different between the two.
The MS6 uses the A-26 transmission, not sure about the MS3.
From the tech notes:
Manual Transaxle Changes
A26 MX-R
6-Speed Manual Transmission
Compact 3-shaft design keeps overall length the same as the 5-speed
manual transmission
Triple-cone synchronizers for 1st, 2nd, 3rd and 4th gears
Double-cone synchronizers for 5th, 6th and Reverse
Wide gear ratios to exploit the engine’s power band
Gearing:
1st = 3.53
2nd = 2.23
3rd = 1.53
4th = 1.17
5th = 1.08
6th = 0.85
Rev = 3.83