It's insane how successful Japan is in spite of their corporate inefficiencies.
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Quitting a job has no complex moving parts, and most corporation will deal with it with minimal paperwork (you really only need to prove you gave them your resignation. An email reply would be enough legally).
The issues these new graduates (the source of the TFA is MyNavi, which is new graduate centric) are facing are arbitrary, purposefuly set to make their life harder.