Hi,
This seems to be a problem with the MagicZoomPlus system which apparently doesn't handle the case where a variant different than the default variant is preselected on the page using the cid.
Regarding your second question, this would require custom code to be added to the MagicZoomPlus system to trigger a modification of the value in the characteristics dropdown based on the thumbnail being clicked on.
Personally, I would handle that differently.
Instead of having all the images for all the variants with only the default image being different, I would have only the image corresponding to the variant in the variant. And I would change the characteristic selection method to "radio" instead of "dropdown" and modify the values of the characteristic to have an img tag of the thumbnails of the corresponding images.
That way, instead of having the thumbnails below the image, they would be in place of the characteristics dropdown, and when you select one, the main image would update.
That might also, in the process, circumvent the first problem.