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The lore fits of the shrines fits so I'm okay with it. It's ancient lost technology so it's not wonder it doesn't fit within the current world. You get told about that right form the start though, so everybody should know about it.
Imagine if all puzzles were in the open world and everybody could do them... wouldn't you question why all the loot is still there? The current state fits the game very well both logically and design wise.