i have both of the 1/0 runs from my alt + to bat + fused, close in to the battery.
the way i figured, in the event of a horrible accident where my entire front end is twisted metal, theres a decent chance that one or both of those cables is severed and/or grounded. while i'm bleeding out of every hole in my body and hoping the jaws of life dont take too long to arrive, i'd rather not be worrying about my battery being short circuited under the hood and causing a fire.
fusing close to the alternator makes absolutely no sense to me. if that wire, which in my case are about 6 feet long since they run along my firewall, is grounded anywhere between the fuse and the battery, you have a short circuit condition with no fuse protection. if you fuse close to the alt, the entire length between the fuse and battery is at risk of a short circuit, why not keep that length down to a few inches?
besides, like was said before if you pop the alternator to bat fuse, its going to charge back through the stock wire (which is fused, by a fusible link or traditional fuse in almost all vehicles... where the hell are you guys getting this shitty information?) not melt your 1/0 lead. a power wire has to lead someplace to conduct electrons... if it stops at the fuse, electrons are no longer flowing, no longer causing any heat, certainly not melting the wire which is no long part of a complete circuit. cmon guys, think.