The tolerance limit is maintained in PO not in Material master..
In PO, you will find the over delivery tolerance in delivery tab,
This option control the over delivery for GR quantity..
Suppose you have made PO with 1000 qty, then you want to do GR for 1050 qty, you can set the over-delivery tol as 5 %, then you can receive 1000 X 5% = 1050 (maximum).. If you give 10 % then you can receive 1000 X 10% = 1100 (maximum).
Regards