I'm not an accountant, but I don't think this fits with Mika's account of events.
1. If Niji was trying to update their tax withholding for contractors, why was this presented to Mika as an
option, instead of a 10% (or whatever %) cut for all the contractors?
2. When pressed for where the money went, Niji didn't say "your JP tax", or "JP tax for your pay". They said "
our tax", then stopped responding when Mika asked them WTF. Maybe they meant "our tax for your payroll", since we only have Mika's words to go on. But Niji's unwillingness to elaborate is baffling - perhaps damning.
3. Mika had lawyers and accountants present her case to the Indonesian tax bureau, and they gave her leniency on the interest, but not the principal. It is not clear whether Mika had
any Japanese tax information from Niji to present to them, or if she only presented her correspondence with Niji. So if Mika didn't have the Japanese tax information, Niji might be liable for not giving it to her. If Mika did have the Japanese tax information, we might infer that it was not possible or worth the time to bring into compliance with tax treaties or recover the money from Niji, based on how the principal was not reduced.
But I agree that contacting the Japanese tax bureau is worth Mika's time. They may or may not care to pay Mika some money back, but that's better than zero odds. On the
side, they might not punish Niji for this specifically, but a company that plays games like this will probably have fallen short elsewhere and might be worth auditing.