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The checkout.liquid layout is available to Shopify Plus merchants only. If your store isn't on Shopify Plus, then you can customize your checkout pages only in the theme editor. Plus, Unlike theme.liquid, checkout.liquid is self-contained and doesn't render any additional template files. This way, even in development the page will not change its style no matter how much you modify it.
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What I meant is that shopify seems to be rendering the checkout.liquid of the active theme when you use 'shopify theme serve'. (as oposed to rendering the checkout.liquid from the development theme you are working on)
Otherwise checkout.liquid works fine, I was just considering to switch from themekit to the new shopify cli and ran into this issue.