Asking the customer to delete a duplicate account wouldn’t solve the problem, as the issue isn’t the customer’s own account, but Shopify’s recognition of the same customer as different people.
As an example: Lisa has never created an account, but she’s placed two orders, one using her email address and one using her phone number. Shopify considers her two different customers. It’s impossible to add her email address to the order with just a phone number, because that belongs to “Lisa #1.” Obviously, since Lisa doesn’t have an “account” there’s nothing for her to delete. And even if she could, what would happen to the order associated with that Lisa? There really needs to be a way to merge Lisa #1 & Lisa #2.