Aww man, the memories of making a garden base for Botania outside my friend's Thaumcraft witch tower, across a river where your could see a Buildcraft quarry running next to someone's industrial complex... Good times!
Tried playing Cobblemon with the idea to make our own themed towns but just like you there doesn't seem to be time for it anymore :(
A nat 20 is the best outcome that the character could manage in that situation, if they have no chance of succeeding then the DM should not be letting them roll. If the barbarian suggests mauling a delicate machine with their mace it's down to anyone else in the party (or the DM if they're so inclined) to remind them that actions have consequences.