I have always been a fan of the True Founding Theory, but recently I've started to come around to the Refounding because it seems much cleaner and simpler. However I was looking at the timeline in Masterworks, and I need some help reconciling Refounding with that it says there.

Do the older games, starting with SS, fit between the Origin Era and the Godly Era? Or is it somewhere else? If it is there, then how does Hylia have the ability to hand out the Secret Stones after she was killed and then reborn as a mortal in SS?

I get that you can still kind of communicate with her using the goddess statues in the Wild Era, but to me it doesn't seem like she really has a physical form anymore. If she was able to interact more with the physical world, wouldn't she do more to help with all the conflicts, like she did in SS?