actually the fuse link will protect the short from BATTERY never from alt. The batt is the only source able to KEEP the short being feeded. If you were running just sourced from alt, the engine will stall on the first instance of the short and that will kill the short instantly, even with 100 amps.

The increased fuse link gauge would be just to support the increased load when a death battery. Bigger alt and death batt will mean the alt will feed and recharge faster the batt with more load. BUT hardly will suck 100 amps unless you rev up hard the engine. That will mean the fuse link will hardly receive the 100 amps load.

14 gauge fuse link will be just fine even with 100 amps alt.

You can increase the load protection BUT you can't go to the extreme because if you get a short, fuse link will never burn, or will take too much time to burn, and damage will be bigger on the short area before the fuse link blows out completelly. Better smaller than bigger on this case.

In Line fuse is a good idea, IF you over rate the fuse to be able to support a peak/surge.