In the complete Bill To / Ship To transaction, two different tax invoices have to be issued. This is to ensure compliances under GST Law and proper flow of credit so that all parties are able to claim ITC. In the present case, the relation between PQR and XYZ is that of a principal and agent, based on the instructions of PQR; XYZ ships the goods to ABC, it will be treated as supply. Tax invoice has to be issued with Bill To as PQR and Ship To as ABC. This is to enable the movement of goods.
The second tax invoice will be issued by PQR to ABC to complete the commercial transaction and also enable ABC to claim Input Tax Credit.
The department in its press issue* released on 23rd April 2018 addressed the issues regarding “Bill To Ship To” for e-Way Bill and clarified that as per the CGST Rules, 2017 either of the party can generate the e-Way Bill and that only one e-Way Bill is required to be generated. The person generating the eway bill will mention the details of his tax invoice.
Therefore, in the above situation, either PQR or XYZ can generate an e-Way bill along with respective tax invoice which must accompany the consignment in order to comply with the legal provisions. The requirement for the other tax invoice does not seem to be in line with the clarification.
* https://pib.gov.in/Pressreleaseshare.aspx?PRID=1529945