Because not too much thought went into the final version of Munch's Oddysee. Self regenerating bombs? I digress. If you want an in-Universe explanation, here's an idea (not official). The Magog Cartel want to clear the Paramite Run for some kind of factory, so they place the explosives down to destroy/scare off the Paramite population in there. The Paramites, however, seem to avoid them. Now, enter Abe aka the player, and it's up to him what happens. He can lead them to the bombs, yes, but he can also possess all the Paramites and move them safely to the part of the Run without bombs. Problem solved from a 'Paramites are sacred' point of view.
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