Adding fuses

If you have your bypass charging wire fused, and have not eliminated the original factory fuse link, then the concern you mentioned should be protected "somewhat." The problem with that wiring, as original, is that the charge output and battery current through there makes it difficult to protect, simply because the original wire size is so small compared to the load

And old story: In the 70's my RR got banged up and I got a Valiant loaner, actually a second one, "after" this story
On a cold morning in San Diego, I was getting off "duty" at the RADAR shop, and hand gone out to start and warm the loaner. A 70's Val slant six. Few minutes later, our leading Chief came in and gave me the "detective Columbo" look. "Say Del, I just have one question. Is it supposed to be squealing and smoking?" So I went out there and the alternator was STOPPED. Turns out a diode had fallen out, and when I wiggled it, the thing SHORTED and I got to sit there and watch the ENTIRE ENGINE HARNESS smoke and fizzzle, after which----it blew the fuse link