It is definitely a good idea to run the alternator output through the battery isolator as well. The Coyote has the alternator mounted down low and out of the way, but just imagine if you're working underneath and swing a spanner and accidentally short it to the positive terminal. I can recall at least three cases where this has happened and completely burnt out the wiring loom as the alternator is usually not fused.

The worst case resulted in personal injury where a mechanic working on a six cylinder diesel rested a full can of penetrant on the manifold. Unfortunately it touched against the output terminal of the alternator and even though the engine wasn't running the full battery voltage passed through the can piercing it and the resulting arcing ignited the contents. Fortunately due to a high level of PPE (underground mining) the mechanic only received burns to small parts of his body despite burning liquid spraying on his overalls and gloves.

Thanks for taking the time to document your build, I am enjoying following along.