I wouldn't say they fill the same roles.
The NCAA is only there to enforce the rules as set by its member universities across 100s of members, at varying levels.
A commissioner can oversee the entire sport and it's overall health, as all pro commissioners do (or even as conference commissioners do in college sports).
The issue is league commissioners are controlling everything right now, to the detriment of the overall sport and other conferences. Imagine the NFL commish saying, "sure let teams move and have the AFC North be a behemoth with 8 of the best teams...and the AFC South can live 2 teams...their fans will probably just die off and stop caring, not my problem as long as the AFC North makes MORE MONEY".
Now, you could certainly have NCAA 2.0 to accomplish this (having a commissioner). No difference, but a new name would be cool