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During his montage of killing/destroying every monster he comes across, there's the scene where Godzilla fights Anguirus, Rodan, and King Caesar, he wins... and then spares their lives, as opposed to killing them. This is a reference to the fact that Godzilla has teamed up with these monsters in the older films from the Showa era, and while those movies and Final Wars aren't in the same continuity, it's ultimately heartwarming to see the King of the Monsters let his past allies live.
The fact that Zilla appears in this movie shows that Toho, while not happy about the negatively-received 1998 "remake", is still willing to acknowledge Zilla as a monster.