You are absolutely right to be confused. This is very common issue with Shopify online sotre 2.0 themes like Dawn, and it’s not a bug in your code. It’s a Quirk in how Shopify handles theme caching and multiple layout source.
Why this happens?
Edit the wrong file: Shopify has multiple layout templates — sometimes, the theme you’re editing in the admin (via “Customize”) is using a different layout file than layout/theme.liquid.
Shopify Page Caching: Shopify heavily caches theme files, especially layout and Liquid templates. Even after you save changes in theme.liquid, the live site may take a few minutes to update — or might still serve a cached version until you publish.
How to fix it properly?
Step 1: Confirm which layout file your theme actually uses
In your Shopify admin, go to Online Store → Themes → Edit code.
Open config/settings_data.json.
Search for "layout": — this shows which layout file your active theme is using.
Example:
"layout": "theme"
or
"layout": "theme.alternate"
→ If it’s theme.alternate, that’s the file you need to edit.
Step 2: Add your meta tag correctly:
Once you find the right layout file (e.g., theme.alternate.liquid or theme.liquid):
Paste your verification meta directly under <head>, e.g.:
Shopify has server side cache.
Sometimes the changes you made in your store are not immediately reflected on the storefront, you may need to wait a little.
For example, I now see 2 both of these lines – one you’ve added recently
and another you’ve shown in your screenshot.
You should remove the wrong one, though it’s possible that Google will be able to see both of them and be Ok with it. Do not remember…
If you’re using the Google & YouTube app (or connected Merchant Center/Google channel):
Shopify typically adds its own verification tag automatically.
If you keep your manual tag and the app’s tag, Google may reject with “incorrect meta tag” because the token doesn’t match.
Fix: remove your manual <meta name="google-site-verification" …> from theme.liquid and let Shopify’s tag stand alone. Then re-verify in Search Console / Merchant Center.