Hi Arno,
Looking at the code, I would ask: Did your score improve by setting accuracy=1 ?
https://github.com/scikit-image/scikit-image/blob/master/skimage/transform/_hough_transform.pyx
Considering that you are asking for accuracy below half a pixel, I would not be surprised if the voting process of the Hough transform is not that accurate. A least-square fitting (Opencv fitellipse) might be more accurate than a voting process for a perfect ellipse.
Aren't the eyeball and the pupil both balls? If you slice them in any way, wouldn't you obtain disks? So why detecting elllipses and not circles? Maybe hough_circle will be more accurate.
Sorry I cannot provide any proof or certitude on how accurate hough_ellipse is.
Kind regards,
Kevin