B, I'm assuming you are referring to an actual fusible link and not an inline fuse, as many people use them as synonyms and refer to in-lines and fusible links as well, but they are different. Using multiple fusible links can be a PIA, especially if you are trying to run them in parallel, or if one is consumed, because as Rod noted, that they all need to be identical to function properly. if you go this route, buy some spares at the onset of your project so you have them on hand if ever needed. There's a reason manufacturers use them, and Rod pointed it out, they're cheap. Using them would certainly work, but I personally am a fan of breakers as opposed to fusing and definitely over fusible links. To Comply with competition rules, I had to (would have anyway) have a circuit interrupter (fusible link, fuse or breaker) between each alternator and battery, and within 24" (this really should be more like 12') of any feed larger than 10 Ga. leaving any one of the batteries. For this reason, there are 5 Breakers in my system.
Some people like fuses so that they can run an oversize wire ga. but limit the amount of amperage through it to "protect" their equipment and will add larger and larger fuses as they add accessories, but the fuse or breakers primary function at this location should not be to protect your equipment, but to, exactly as you mentioned, protect the vehicle from damage or a fire in case of a dead short between the alt and battery, and battery and the rest of the vehicle. Because of this, the breaker/fuse should be sized for the ga. and power handling of the wire, not of the accessories attached to it.
hope this helps.