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Just so I understand, you are concerned that the paths aren't right on top of each other? Are you visualizing in top down ortho mode in rviz?

image description

Check the Z coordinates of the EKF output and the navsat_transform data. And are you sure the straight-line segments line up? It's a line, so it's impossible to say from your image whether the poses are offset from each other.

And what static transform are you not certain of?

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