Why is it a thing? Everything else in aviation seems to have good amounts of checks, balances and buffers. It feels the same to me as skimping a couple percent on fuel or doing less frequent maintenance. Both also reduce turnaround time.
This runway was over 2 miles long. If you are in a smaller commuter prop plane or small jet, you don't need half that space for the takeoff. You call up ATC and they give you the option of taking off at an intersection now, or being #15 in line behind the heavies, its totally fine to do that if you are within the operating margins of the aircraft. The pilots have already done the math to know exactly how long of a runway they need for the worst case scenario (rejected takeoff just below V1), so if they know that they need 5k feet worst case scenario, and are offered an intersection takeoff with 7k feet of an 11k foot runway, there is already pretty big margin built in.
The thing to remember is that the aviation community and manufacturers have decided that once a jet is past a certain speed, you are committed to taking off and climbing out no matter what is going on. There is no circumstance where airliners will go beyond that speed and then try to reject the takeoff, and land back on that same runway.
As far as fuel, you might be distressed to know that you rarely fly with full tanks. They typically fly with the amount of fuel their route uses for the load they have + a margin for diversion. This is both a cost savings measure, as well as an operational concern (for example at Denver during a hot summer day, a lot of planes can't be loaded to maximum weight and still be able to do a rejected takeoff)
Was flying as a passenger on a really small airline (8 seater plane, Green Air) out of San Jose in Costa Rica. We got cleared for takeoff ahead of a United 737, at most 500 feet into the humongous runway for that plane. Yet the pilots still put in the 2 minute effort to taxi back to the beginning of the runway, even though they could have easily taken off from where we entered it. Don’t know if it was their protocol or the pilots decision, but I will trust this airline for a very long time.
I imagine in a while we will all be able to read the investigation reports, since the aircraft crashed shortly after take-off the black box recorder should contain all the information we need to figure out most of what happened including possibly the reasoning for the decision to make an intersection takeoff.
Now, obviously there's a discussion to be had about where the line is and what should and shouldn't be standard operating procedure but there's basically no safety improvement to have even a fully loaded 757 or Learjet or whatever drag it's butt to the very end of a 15000ft runway.
A pilot may be trying to scoot out of there ASAP because he knows based on the radio and who's where that's gonna make everyone else's jobs a little easier. An airport is run by professionals all of whom are trying to make things run smooth. It's at the complete opposite end of the spectrum from a school or Starbucks parking lot.