The advantage of connecting the S (sense) wire directly to the alternator output is that it measures the output voltage directly, and eliminates a bunch of old, problematic Samurai wiring. If this OEM wiring is the least bit faulty, the alternator output will fluctuate and could easily overcharge the battery. But, you must have the heavy gauge (#6 or larger) new charge wire going directly to the battery in any case. Without it, you will surely blow the OEM fusible link, sooner or later. [The disadvantage is that it controls the vehicle voltage slightly less precisely, with about ¼ Volt of sag at 100A. A large heavy charging wire helps to minimize this effect.]
If you can fuse or otherwise protect the new heavy charge wire, so much the better. The largest MAXI fuse is rated at 80A. If you draw 100A for only a very few minutes at a time, you could be OK with a single fuse. If you expect to draw 100A for very long, or if you blow the fuse frequently, (they only last a short while at full-rated current -- that's hours, not years), you could use two fuses in parallel, right at the battery, with a few inches of smaller wire (e.g. #12) for fuse lead wires. The few inches of smaller wire helps to equalize the fuse currents. For 100A, the total fuse ratings should add up to over 100A so your fuses will last. Two 60A or 70A MAXI fuses in parallel should work OK. I'd carry spares.