Sega gets just as much leeway like Namco did when they both joined forces with nintendo for the tri Force thing. i wouldn't say sega has more leway just because they're sega but MARIO AND SONIC pretty much made them more important recently.
Anyway miyamoto when advising Amusement Vision on F Zero had a big bust up with Nagoshi with the way the game was headed. So i don't think he's necessarly a big fan of Sega and their work ethics as such. Although he and naka are good freinds apparently.