Earth = Poison is a really dumb side effect of the way they decided to arrange and categorize the skills.
There would be nothing stopping the mushroom spores become exploding corpses or other Necromancy themed stuff to put those skills there, and have it work that way.
Hell, they might as well add an extra skill group called "Venomancer" or something just for poison related abilities, since there's enough of those from the previous game to spare, while keeping Geomancy about earth and fossils.
