Yeah, Japan has ruined me for public transit in the US and elsewhere. Clapping on a plane would just make me annoyed unless the pilot did something phenomenal in a bad situation or the like.
It makes sense in a time without autopilot and the pilots actually had to fly the while time and sometimes really wrestle with the controls. Now it's all automated so it's not nearly as impressive.
I'm no expert, but I'm fairly certain takeoff and landing is still fully manual. Autopilot only happens once you hit cruise altitude where the risk of crashing is very very low.
OK yes, pilots are waay overworked because of the limited number of them. That has nothing to do with actual flying
Edit: From your article - “Concern over pilot fatigue was one of the primary reasons that ALPA was created back in 1931, when operators regularly engaged in ‘pilot pushing,’ forcing pilots to fly long hours to maintain demanding schedules,” said Capt. Brian Noyes (United), chair of ALPA’s Flight Time/Duty Time Committee, which is responsible for educating ALPA pilots about the risks associated with fatigue and the regulations and safety programs currently in place to help mitigate those risks.