Same issue. Tried to upload the JSON file through “content” → upload files → get LINK and then create a URL link through Online Store → navigation → Create external url link and link the /.well-known/assetlink.json to the URL link given by shopify for the JSON file. When browsing to the URL link directly as given by shopify, it opens in the browser and you see the JSON code, but when you use the redirect URL (the one Google would access /.well-known/assetlink.json, then the file is downloaded by the browser instead of “streamed”, so Google doesn’t recognize it properly.
Ugh!