If they were planning on doing a GPS approach then they might not have even tuned up the LOC with associated DME. The only distance reading would have been to the threshold from the FMC. This would have left them low instead of high.
I know it's a bit far fetched but..... stranger things have happened.
Well, this early in something seemingly inexplicable, almost nothing can be considered far-fetched - including sudden crew incapacitation. However, usual practice is (or should be) to use all available navaids. That would include, if possible, using VOR radials to cross check the IAF at COLIG, as well as a time hack at BASKN to time the segment from the FAF to the MAP. But I'm not sure why having an exact readout of the distance to the threshhold (LOC DME minus 1.3) would necessarily result in flying lower-than-published approach altitudes - for any of the RNY 18 approaches.