I ran into this same problem. From what I found, looks like the Metafields2 App is making POST requests to the /variants/#id/metafields.json endpoint. And the product update webhook doesn’t fire when using that endpoint.
When I make a POST request to this endpoint, the webhook doesn’t fire: https://knack-production.myshopify.com/admin/api/2020-01/variants//metafields.json
{
"metafield": {
"key": "test",
"value": "test",
"value_type": "string",
"namespace": "global"
}
}
Here’s the API reference for this endpoint: https://shopify.dev/docs/admin-api/rest/reference/metafield?api[version]=2020-01. There is reference to updating a variant metafields in that documentation
But when I make a PUT request to this endpoint, the webhook does fire: https://knack-production.myshopify.com/admin/api/2020-01/variants/.json