Hi,
Purchasing organization is considered as reporting unit but why you want to control Tolerance limit based on Purchasing organization?
For LIV, the tolerance keys (AN,AP,BD,BR,BW,DQ,DW,KW,LA,LD,PC,PP,PS,ST and VP) set with Tolerance Limit at company code level in t.code:OMR6.
If business needed, you can create Tolerance group for vendor in t.code: OMRX with your company code and Assign Tolerance group to vendor master record in t.code:XK02 in “Payment transactions” view.
OR
Check to use Enhancement MM08R002 and discuss with Technical consultant for necessary coding for your requirement.
Regards,
Biju K