The nature of commercial flying is such that actual incidents are pretty rare (150 or so a year recently[1]), and very very expensive. So taking the "data-driven" approach to pushing what's safe really isn't economically feasible, to say nothing of the ethics issues. Instead the principle of "if it seems unsafe, it's probably unsafe" applies. I believe the situation mentioned in the article of riding for fourteen hours then flying for nine is allowed by the FAA, but if the pilots aren't rested (reasonable after riding in a cargo plane for a day), then the airline shouldn't be asking them to fly.
A crash of a cargo jet (eg. converted airliner approx. $40m value) is such a rare event that "bean counters" can justify a certain level of risk.
A good comparison is SpaceX Falcon[0] or Orbital Sciences Antares launch vehicles. If they have a mishap, there is high probability that it'll take 6mo+ to return to flight. There is a significant cost to that ($300m+ cost to SpaceX, for vehicle replacement and compensation for delays). If UPS crashes a jet due to pilot fatigue[1] and nobody on the ground is hurt, the airline will continue flying with minimal interruption.
There have been issues with Fatigue causing accidents at both UPS[1] and FedEx[2]. If a cargo jet crashes but doesn't cause ground fatalities, the general public forgets fast. The UPS Airbus A300 crashed in Birmingham, AL with 'only' two crew fatalities. A passenger A300 would likely have resulted in many more fatalities.
Turkish Airlines had a cargo 747 crash[3] in Kyrgyzstan, killing 4 crew and 35 people in the village that it crashed into. This involved a contract operator, and received minimal attention in the world media.
In aviation there is a tendency towards "regulate by tombstone"[4] When an El Al 747 crashed shortly after takeoff in Amsterdam and killed 39 in an apartment complex, along with 4 crew, It was a huge story in the European media.[5] 747s were inspected, repaired and upgraded to prevent a recurrence.
Cargo airlines do a lot of "back of the clock" or overnight flying, which is considerably risky from a fatigue point of view. I'm actually amazed that more accidents haven't happened.
Someone needs to quantify the cost for various level of risks. If the air cargo industry could save an average of 1 live per year at the cost of $1B a year in additional costs to pass to it's customers, should it?
[1]: https://en.wikipedia.org/wiki/Aviation_accidents_and_inciden...