Simply copying the files across should NOT be considered a true preservation/archival-grade copy of the disc any more than ripping a standard audio CD to WAV with iTunes should be considered a proper rip of that disc.
Can one recreate a completely identical copy of the disc by burning from said “copied” files? No? Case closed.
My current method for discs with data tracks is to use ISObuster to rip the raw data track as a .bin file, after already having ripped the audio portion of the disc with EAC.
Since the cue sheet can point to this .bin for the data track in its appropriate location, theoretically there should be a way to properly burn the full set of audio+data .bin track back to disc, offset corrected with proper gaps, indexes, emph flags if necessary, etc, however I have not gotten so far as to find a way to actually do that.
In my perfect world, EAC would already handle ripping this correctly with little effort needed on the users behalf, instead of completely ignoring the data track as it currently does.