I think there are 3 sets of variables at work here:
Poor egg collection and packaging vs. excellent collection and packaging.
Poor incubation practice vs. excellent incubation practice.  As mentioned, some folks buy shipped eggs without having any experience with incubation management.  They toss the eggs in the bator, believe the readings on the thermometer and hygrometer, never calibrate equipment, even follow the often pathetic hatching instructions that come with the bator.  They don't know how to candle an egg, are not familiar with the bator, don't check for warm/cool spots.  I could go on and on about how folks mis-manage their incubation.  An experienced hatcher will make adjustments to accommodate for porous eggs, large air cells, saddle or misplaced air cells.  
Shipping:  I live at the very end of the line, no matter what is being shipped, or where it is coming from.  Be it eggs or chicks, they receive rough treatment and spend a LONG TIME in transit.  I believe my last shipment of chicks had 3 separate flights before arriving in Maine.  They missed every single connecting flight, which resulted in adding DAYS to their travel time.  Every leg of such a journey results in being handled in not very gentle manner.  I did try 2 batches of shipped eggs.  One came with multiple smashed eggs in the box, in spite of being bubble wrapped.  The second box had a few cracked eggs, but hatch rate was still poor by my standards.