There are two types of vouchers... Amex Taj vouchers and Taj experience vouchers.
Taj experience vouchers work on all fare types. Discounted also. No issues
Amex Taj vouchers are little restrictive as some hotel properties do not allow them against discounted rates. Some city properties where there is good competition, Amex vouchers are accepted on discounted rates also (but no guaranty, better to check with property). Resort properties will mostly not take Amex Taj vouchers on discounted rates.
So you need to be careful if you get vouchers via Amex. For regular Taj experience vouchers, there is no issue