There was no change to the digital side of things in the SE version of the Oppo player. All they did was beef up the DACs and a few other minor parts of the analog chain.
If you're planning to use the HDMI interface, then there's no reason to get the SE upgrade. If you're using the analog 7.1 output, it's time to get a new receiver rather than the SE upgrade.
While I believe that decoding to PCM in the player is the right thing to do, after that it should be passed digitally to the receiver so any room correction (even if it is just delay and trim, if you don't like EQing and the rest of that stuff) can be done by the receiver. The receiver drives the speakers, so it should make the output adjustments. Imaging if you had to calibrate each source component. That way madness lies.
