First of all, Kudos to PG and Apurv for taking up this matter at such a short notice and getting the real story out.
I still feel there is something more to it than what meets the eye. If the institute, at some point in the course of their admission process decided that it would accept XAT / GMAT / CAT scores as well, they could have emailed the applicants asking for their XAT / GMAT id. The student can go and update their XAT / CAT registration numbers. Also, those who had not submitted their application forms can mention their registration numbers alongside CAT registration numbers. This is exactly what SPJIMR did.
But now, the say, they would refund the extra Rs.1300 taken from applicants. Those who secure admission, will get the amount adjusted with their term fees!! This means that the refunds wait till the GDPI results are done / forgotten! Why still drag the issue, refund the application fees to all, and charge the successful candidates a flat slab fees!