We were discussing the same thing in our office. QNE in SDF was about 3009 and about 2996 in BHM at the time of the accident. Could lead to lower than indicated, and possible instrument error too
I think you mean QNH, not QNE in SDF and BHM.
If it was never reset to QNE (STD in the 'bus) after takeoff in SDF, they would inevitably get a call from ATC when leveling off in RVSM airspace enroute.
But, as you conjecture, if it was switched back out of standard and then never reset from the SDF QNH, the path guidance on an RNAV (GPS) approach would indeed lead to a point short of the runway.