Nick, independent crossover settings for each group of speakers is generally a very desirable feature. It could be argued though, that if all the speakers have similar bass extension and aren't in positions where the room affects their bass much differently that a global setting is adequate.
No well-designed receivers have an inherent "sound"; it's features such as tone controls and room EQ which change the sound.
All auto-setup systems adjust the level of all speakers and the sub so as to be uniform at the listening position. Room EQ is separate from calibration for levels and there the Pioneer is unacceptable in my view because of its lack of provisions for the sub. This more than outweighs for me the flexibility in other areas with MCACC which allows the user to screw up the sound. I would choose an Onkyo or Denon(Marantz is simply an overpriced Denon)receiver with the highest grade of Audyssey which the budget would allow.
