The checkout is the product. Everything else Shopify sells can be replaced — the theme, the admin, the CMS — but the step where a stranger types a card number has been tuned against more transactions than any team could reproduce, and giving it up is how headless builds lose money while looking more modern.
Which is why the headless path keeps the checkout: a Nuxt front end against the Storefront API, handing off at the last step. The same shape as AEM content on a custom front end — own the experience, rent the transaction.