Here's what really happened:
Stern aquired the license to the upcoming Godzilla WARNER Movie, then heard of Spooky/ TOHO and blew the party.
While I don't know if they're intending to do a "limited edition" Version of Godzilla with the Toho license ore just don't want to be 2 Godzilla Pinball games around at the same time I don't know.
Source: Common Sense, since it would be money thrown away any other way. And Spooky will sell their 500 games of whatever they produce anyway, so it doesn't matter (to Stern) what license they get.