Hyde here from Shopify.
Could you tell me whether you bought your domain from Shopify or from a third party?
When you buy a custom domain through Shopify, the domain is automatically configured to be your store's primary domain. It may take a few hours to fully propagate, so there may be a delay in the SSL certificate being issued.
If you bought your domain from a third party, then you will need to configure the DNS settings to point your MX records to Shopify. Only when the domain is properly connected can Shopify issue an SSL certificate. If you're unsure how to do that, there's a guide right here.
I hope that helps! Let me know if you have any other questions.
All the best, Hyde.