I don't recall Toho ever saying Legendary can only make three films. It was simply confirmed that Legendary had "greenlit" Godzilla 2 and 3.
Plans may have changed since then. We don't know if Godzilla 3 is Godzilla vs. Kong or something that will come after yet. Ultimately, I think the Legendary Godzilla series after Godzilla vs. Kong entirely depends on the box office. If it makes a great deal of dough I'm sure Legendary will find a way to continue. If not--Well, we'll see.
Either way I'm not too worried about it. It's becoming increasingly obvious that whether it or not it comes from Hollywood or Toho, Godzilla won't end.
"'Nostalgic' does not equal 'good,' and 'standards' does not equal 'elitism.'" "Being offended is inevitable. Living offended is your choice."