Animal Crossing, Stardew Valley have a lot of great game mechanics and are also about discovery, trade, and building relationships. Factorio is probably a bit more advanced, but meets your criteria (except for story, maybe). There is a rabbit hole of games like that to go down. Assassins Creed Origins and Odyssey have “education” modes that are about exploring the world and not murder. The Mario-plus games (Tennis, R…
I don't think Factorio counts as non-violent. You might be able to make it so via some settings but that would remove a big part of the gameplay and challenge.
That's subjective! Personally, having the biters enabled removes a big part of the gameplay for me as suddenly I need to focus on being able to defend myself, while for me that game is about building as effective factory as possible.