Good news: the IND has adjusted the frequently asked questions list regarding the ICT permit for Japanese passport holders (https://ind.nl/en/Documents/ict-richtlijn-faq_ENG.pdf):
Q: Do other conditions apply in terms of assessment to persons who have the Japanese nationality, given the Netherlands-Japanese Trade Agreement?
A: It is not obligatory to apply for an ICT permit when a trade agreement can be invoked. In other words, one may choose. Persons with the Japanese nationality could also apply for a residence permit as highly skilled migrant or a work permit based on paragraph 24 of the Foreign Nationals Employment Act Implementation Decree if they meet the conditions for one of these permits. No other conditions apply, if an ICT permit application is submitted.