A further note here, I see that there are some other, much older threads discussing something similar, although without (public) solutions:
It would make sense as a multithreading issue as one of those posts mentioned that the issue would go away if you set thread count in the pathfinding settings to 1. IE one thread starts using that native array of tag penalties before another is finished with it and you end up with max int penalties applied, or something like that.
I am not using AlternativePath script as far as I know, as some of those threads mention, only a custom ai lerp script.
One reply there mentioned just editing the GraphNode.Penalty property setter to just throw a warning but otherwise edit on Setting the Penalty to a normal number if it is > 0xFFFFF, which I guess would work but not really fix the underlying issue. Does a newer version of astar address this one way or the other?