Vanilla is right, the VAT registration status of the purchaser has nothing to do with the stamp duty. Pure and simple, stamp duty is charged on the VAT-exclusive amount, S48 of the Stamp Duties Consolidation Act.
The majority of investors would not be VAT registered anyhow, particularly with residential property, as short-term lettings of less than 10 years are VAT exempt, unless exemption is waived. If exemption is waived the investor can take an input credit for the VAT suffered on the purchase but must then charge VAT on the letting. Not many tenants would be willing to pay VAT on their rent.