Neither of these methods protect against overvoltage, only reverse polarity.
If you use a zener diode in the place of D1 above it will protect against overvoltage and reverse polarity simultaneously, but it still has the same shortcomings of a regular diode to ground.
You can jumper the diode when it is in series to bypass polarity protection and the circuit will work fine, but will have no protection against reverse polarity.
You can't jumper the diode to ground, but you can remove it (or omit it) completely. Again, the circuit will work fine but will have no protection against reverse polarity.