The only reason to have the diode in parallel is if you can't afford the voltage drop from putting it in series. If you have a 12 V supply and an 7805, the 7805 needs about 7.5 V to work. With the diode that gets to about 8.2 V, so on a 12 V battery it's fine.
Having the diode in parallel you are relying on the fuse blowing before the diode. That is really dodgy as you should consider all voltages up to the maximum supply voltage. You can get the situation where the diode is OK with a good battery, but not with a flat battery, where you could get a low current for a long time.