I'm not clear on the point of why the speaker calibration would be any different from the two channel setup (R/L) to 5.1 or any other mode! Maybe the level would be different, but if you set the channel calibration with a SPL meter and they are all at the same reference level, what does it matter?
If the sound field seems out of balance, wouldn't you raise the calibration level of either the right or left speaker to compensate for this? I have a left front speaker that has to be raised 2db more than the right one to match it in ouput, I don't know why, but all my speakers match in level, which would seem to be the most important thing.