It now makes sense that Shanks and his crew were in some remote far off part of East Blue after stealing the thing. The only way it makes sense from a World Government perspective is that if they didn't know Shanks and Luffy came into contact, they probably believe Luffy had the legit Gomu Gomu no Mi. Though I think they should've probably been curious after Enies Lobby when he was fully on their radar. Still, it's a tremendous oversight for them to not consider Luffy was rocking this fruit until THIS FAR into the story.
my understanding is there is no "legit gomu gomu no mi". there is only the hito hito no mi model nika, which is known to everyone else as the gomu gomu no mi.