I know its been a while since this was updated, I wasn't just ignoring the issues but spent far too long trying to find work around's for a system that was never designed to work this way but I was persisting with it because it was lightweight in comparison to the only other obvious solution.
I eventually gave up and come up with a new system that is faster to process then the previous one which is still using the Navmesh for navigation but it is no longer using a NavmeshAgent to move around on it. This fixes all the bullshit issues with animals doing whatever the fuck they want, yay
I also fixed the typo that was making all animals invincible