If you are using Shopify as a core ecommerce platform, but have rolled-your-own storefront (not using Liquid templates) then Littledata's app can still track the complete customer journey.
Our tracking works with a headless store because our app gets webhooks for checkout updates, orders, refunds and more that trigger events in Google Analytics (or Segment), even if the tracking script is not on the checkout or thank you page.
The part of our storefront tracking script that you need to implement yourself is to get the client ID (the cookie identifier) from the pre-checkout page and send it as a checkout attribute to Shopify. This enables our app to link the pre-checkout user session with the webhooks from Shopify.
We've built a Demo Headless Store to show you how that works.
Other checkouts, like Recharge, need to be initiated using a Shopify cart. In this case you'll need to add the clientID to the cart attributes before sending on to the checkout.
And example with Recharge is included in the demo.