>>39668881They're only the publisher outside Japan now.
TPC is the publisher that matters.
Also, Game Freak owns TPC, not the other way around so TPC despite being publisher has no control over Game Freak. Masuda would be in control of the deadline as the producer and a member of the board at GF.
Saying Nintendo has control over the development of Pokémon is like saying Headup Games has control over the development of The Binding of Isaac, just because they do the publishing for it in Europe.