Something that bears mentioning here too, since one of your examples used water: the server-side maps don't have water areas. The server has absolutely no idea where water is in the zone.
I have no clue of the technicalities behind the S3D files or the resulting MAP's that were made from them, but I'm gonna guess that if it was easy to extract water from the S3D's, the maps would already have them
In your example, the mob probably would've gunned straight for the player, swimming through the water, as the server wouldn't have seen the water as a barrier to LOS. But contrary to what you seem to suggest, that's actually normal behavior in a lot of EQLive zones: mobs aren't afraid to get a little wet if it means some xp from that juicy player kill :P
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