Is the insignia on Payload's arm (version 1 and 2) supposed to be a mission patch or is it a NASA logo? I tried looking at NASA patches to compare but my figure's logo isn't quite mint so I can't tell.

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I just looked at both figures under a magnifying glass. There are no real letters that I can see. It looks to me like more of a mission patch because in the upper half is a basic shape that matches the outline of the Defiant shuttle shape rather than a real shuttle. So I would guess mission patch.