A very basic newbie question

Always follow the instructions in the .pin file regardless of the setting for unused pins.

You still need to follow the instructions in the .pin file with the unused pins set to "As input tri-stated". The .pin file probably tells you to ground unused pins. If they are left unconnected, the input buffers will float. That can cause oscillations on input buffers, which can result in a high I/O current, noise, and degraded reliability.

For device families that have the option "As input tri-stated with bus-hold circuitry" for unused pins, I recommend that. For device families without that option, I recommend "As input tri-stated with weak pull-up resistor". With either of these settings, it is OK to leave unused pins unconnected and also OK to have them driven either high or low by something else on the board.