Based on "MC9S12ZVC Family Reference Manual" commands to set user/field margin level both take "global address to identify flash/eeprom block" as one of their parameters.
Should the address be the beginning of the block or any address in that block range?
It can be any address within the block.
Are you ready for flash/EEPROM ECC exception handling? Modified margins may lead to uncorrectable ECC error and trigger not maskable exception handler... I guess you are doing it for better memory integrity checks, so please don't forget as well to implement and virify operation of exception handler and of course return from it ;).