You don't have any XLR cables to try for yourself? If the Sony is fully balanced then yes you will hear a significant improvement. I have a fully balanced cdp, Cary 306 Pro, going into a VTL 6.5 preamp, also fully balanced, and the difference was like 50% better w/ XLR.
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It has a balanced output and it's done correctly. The SCD-1 was not done correctly.
I have mine connected to a BAT VK-50SE preamp - it only allows XLRs, and of course, is differentially balanced. I hope you can try connecting the balanced outputs of your 5400 to your preamp. I'd like to know if you perceive a difference.
I've had a Sony xa-5400es for 7 months now and ran Audioquest King Cobra RCAs for a couple of months then switched to King Cobra XLRs and it made a noticable difference in sound through my McIntosh MA6900 and PSB Synchrony Ones. It is interesting that the system plays louder through the RCAs but sounds smoother with the XLRs.