For non-Shopify Plus merchants, there is no way to add any customized input boxes on the checkout page, and for B2B customers, it is difficult for merchants to collect their VAT numbers.
We check the content of the Company field and if the Company field does not contain a VAT number, an error message will appear below the Company field telling the customer that they need to enter a VAT number in the Company field, we support all European VAT number formats!
Make sure you set the Company field to be visible in Settings → Checkout.
Note: The rule check is triggered only after all Delivery fields are filled in.