Hi,
You can maintain exemption % in vendor master but there is no feature to define the limit and deduct tax as per the limit.
You can meet this requirement by defining formula in the path IMG - FA - FA Global settings - WHT - Extended WHT - Calculation - WHT codes - Define formulas for calculating WHT.
Here you can define the reduced tax rates and exempted amount to be deducted for the tax type & code combination.
Regards,
Jyoti