Emile responded to my questioning (generalizing from here on) certain aspects of files that he expended a great amount of time and energy minimizing impact. The amount of compression that may have bogged down older hardware unpacking is trivial on an Extreme. File handling (embedded pictures etc) should also be no source for concern.
Opinions vary widely on if older or lower quality optical drives provided the best possible rips back when or currently. You can always select a few albums and use a collection of hardware and software you feel offers the highest quality and rip them to WAV.
I have suspicions older files and especially those transferred around over the years lose magic. Nothing lasts forever. Including strategies to provide storage for an entire library of ripped files, in some homes.
The differences I hear are with the extreme's extreme cpu hardware and yet local FLAC sounds degraded. It really can't be just the hardware power as you note, but something is still going on.
As for old files/rips, my WAV file is about 4-5 years old and sounds great. The FLAC made from that WAV a few days ago does not sound as good, so I don't see age of rip as a factor.