I think that you have the labels reversed for turning on cross-eyed and wall-eyed stereographic views under the style option. In order to view a stereo display of the molecule using cross-eyed viewing, I have to select wall-eyed on your option list. For cross-eyed viewing I look at the right image with my left eye and the left image with my right eye. If I do that with your cross-eyed option the distant atoms visually occlude the nearer atoms. Either the labeling on the views is wrong, or the rotation matrix is applied wrong -- which of course gives you the same result.
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