I hope Im understanding your question. If you leave the auto flag detect on it will enable the rear center for flagged material only. From what I have heard not all dvd's are flagged. If you leave it off you have to turn it on each and every time when there is rear center material present.
If you leave auto-detect OFF, then you have to manually enable 6.1/7.1 when you are playing EX/ES material.
However, if you set it ON: - It will automatically turn on your rear surrounds when it detects the flag. - If it does NOT detect the flag, it will work according to the option you set for non-flag material.
On my 3802, I turned it ON, and set non-flag material to be played in matrix mode. So actually everything I play comes out in 6.1 for me. 5.1 material gets matrixed.
The 3802 has a button on the remote you can use to switch on the fly with auto detect off. The button will cycle through sb off, 6.1 including matrix for non 6.1 material, and sb non matrix which plays the signal through the side and rear surrounds.