I've launched a few Shopify stores recently and Apple Pay has not worked out of the box with Shopify Payments.
Here is the issue I received along with the status code 417 (taken from debugger) of the failure:
The only solution for this according to Shopify Support is through their tech team. If you're getting the same issue please continue to press them to resolve this issue on their end. I do not know why, but Shopify Support continues to find ways to make my clients waste time doing things that are not relevant.
See the screenshot below for the support team member who helped me resolve the issue and his notes.
More notes that show this is a known bug, but for whatever reason they continue to make you work in circles for it.
I wanted to share this somewhere so as to help those who run into this issue and can resolve it in a timely manner, rather than the roundabout way I had to go to get here with multiple Shopify Support team members.
If there is a good way to avoid this, I'd love to hear it.