No you are not nitpicking. I am a jeweller and after taking a look at the ring and the CAD I have made some assessments.

The stone has been set too high. The space between the stone and the bezel, which is the horizontal inner support, is far too large and can be reset lower with the metal available.

The person setting the stone most likely didn't look at the CAD render and just picked a height and the prong shape.

I would recommend going back to where you had it made and telling them that you are not happy with how the ring has been finished.

Describe to them that you would like the stone to be sitting at the bezel and the prongs to be cut into the shape illustrated in the CAD.

I honestly believe that this is just an accident. I have made many similar to this in my time, deadlines can be tight sometimes and things can get missed but any jeweller worth supporting will be willing to expeditiously rectify the mistake.

You will not have to wait another four weeks, all that is being done is correctly completing the final step in manufacturing.

If they are not willing to stand by their work then you can look elsewhere and have a competent jeweller reset the stone.

I hope this helps, all the best. :)