I think the team tried to rationalize this decision because of Mechagnomes obvious disconnection to the nature and elements.
I personally never liked Goblin shamans (although I started leveling one and stopped just to reserve the class for my Vulpera and because I hated their totems) but honestly - I am with you on this. They already established it in the lore and told us goblins are not asking the elements for help but are in fact using them. So I see no real reason why Mechagnomes shouldn't or couldn't do the same.