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No, Nadir Adaptor on NN5 will not change the settings. Using NN3, you have to reduce the Lower Rail Setting for 6mm because off an offset with NN3 Vertical Rail.
Having done your turn around stops, go down to -90° to shoot the first Nadir shot. Then open up the adaptor, and move the tripod aside to the opposite direction. The minimum distance to move is double the distance from Rotation center of the rotator to pivot point of the adaptor (below the screw). Then take the second Nadir shot. On the pics there has to be free space between the 3. tripod leg in first shot and the corner of the adaptor in the second one.
In PTGui you use the masking function to mask the tripod in the two nadir shots and the go on stitching.