Is it required to program microcontroller with parallel port for the first time
It is basically as you say.

The built in token ISP program supports programming the device through a default interface. This should then also allow, if I understand the datasheets correctly, to change all those parameters to change the ISP procedure.

However, this is a question you should ask inside your company, since it is much more likely the default interface(s) are used incompatibly on the end board. While you'd usually favour keeping one default interface available through the board, it is possible in this case that wasn't possible.