Liz,
The most important thing about the vertical position of the skimmer is that when the water is in the middle of the waterline tile, it also needs to be in the middle of the skimmer's mouth.
When I look at your first pics, it appears to me that when the water is in the middle of the waterline tile, it will be at the top of the skimmer's mouth..
This means that your skimmer will not skim.. Yes, water will go in and back to the pump, but you will not get any skimming action.
You are not going to be able to fix that by adding tile or a collar for the lid.
Your pool builder needs to actually come out and see the problem.
Thanks,
Jim R.