There is not root in the common sense like if you were self hosting a website or CMS.
The service asking for verification should be able to provide a meta verification tag that you can add to your themes theme.liquid file in the <head> area of the code.
See https://help.shopify.com/en/themes/customization/store/verify-domain-with-third-party-services
A workaround is adding it to the themes assets files, then using {{ '.txt' | asset_url }} in your theme to get the url where the assets is available online.
Or the admin files and use the file_url filter instead
Then in the admin setup a navigation redirect to to point from the "mydomain.com/.txt" to the actual asset url, results will vary.
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