Airline pricing is incredibly complex because...it is a complex product. It's a perishable product, and they are trying to price discriminate multiple classes of people, dealing with competitors, etc. It is very common to have the case he considers rare (XXX-YYY-XXX costing >2x what YYY-XXX-YYY costs -- especially international, where different currencies, taxes, etc. apply). XXX-YYY often costs 4-8x the cost of XXX-YYY-XXX or YYY-XXX-YYY r/t, too.
There are certain routes which are run as "air shuttles" -- you can buy a ticket, and then walk on and get on any available flight. SIN-KUL, IAD-NYC, etc. Some airlines have very simple routing and fares (Southwest, for instance) and can more easily be used for flexible travel. First Class or Full Fare Coach tickets are also used by businesses or other travelers who demand extreme flexibility -- the $170 r/t SFO-LAX-SFO was a discounted coach fare where price discrimination in terms of restrictive terms applies.
Additionally, airlines are highly regulated, some by international treaty (read the back of a ticket jacket sometime).
As for "not screwing a major customer over", a frequent flyer would be 1K or GS and worth $50k+/yr to the airline, and would probably have been able to easily get his ticket changed. Yes, price discrimination and market segmentation sucks when you lose the game, but it maximizes revenue for the carrier.
Btw, the "hacker news" of "airline hacking" is flyertalk.com. There are people who craft amazing itineraries and maximize frequent flyer points in ways which seem absurd (scheduling 4 r/t back to back flights across the US to Hawaii just to get miles, or flying SFO - Taipei - LAX for the cost of SFO-LAX to get huge extra miles).