No one actually said Abe travels through upright, the way he went in. For all we know he tumbles around inside like a ragdoll, but it is not the sort of ride I would expect of the mudokon techsperts. Perhaps he curls up and spins inside like in the wells of MO.
I do think it is a natural phenomenom, with the answer deep inside the planet. We all know abot water cycles and nitrogen cycles etc on Earth, how water can end up underground for thousands of years before it reaches the sea again. Perhaps the wells are natural passages of an air cycle, and the mudokons simply built well tubes as a way of exploiting the force. And the industrialists would have realised the hard way that blocking them of is detrimental to their facilities (KABOOM!) so build them into the floor. Doesn't explain the wells in Vykkers' Labs, though.
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