Aside from retconning Magical Mystery Cure so that Twilight was a less capable new ailcorn, Discord a less tamed cosmic-level prankster post Keep Calm and Flutter On, what I got out overall of the two part season four opener was that ponies were not responsible for creating the Elements of Harmony. That if griffons, dragons, diamond dogs or even changelings had managed to discover them, use them and express their own idea or view of "harmony", Equestria would have been a different place.
Course I noted the sun and moon marks on the tree before they were lit up at the conclusion. Lingered on the earlier headcannons before settling on one set towards the presented evidence.
By those marks Luna and Celestia are connected to the tree. Are likely immortal and have their powers because of it. The tree itself may even be the proto-Element from Hearth's Warming Eve. A "seed" grown into a tree involved in the creation or birth of the Sisters and even involved somehow with Discord. Clover the Clever and Starswirl the Barded researched the proto-Element, inadvertently "plant" the tree causing the Sisters to also be brought into being, Starswirl casts the Magical Mystery Cure spell transforming into Discord over time, and eventually the Sisters are forced to take and use the Elements from the tree to stone him. After like most proper wizards he's already set counter plans into motion.
That reassembles much of my own prior headcannon. Makes ponies the creators of the Elements again.
Further want to put out that when the Sisters took them from the tree, that the Elements probably weren't "ripe" or refined. Which was why only Celestia could use them when they had both used them before, and why she and Luna lost their connection to them after the Nightmare Moon incident. That they became refined after the Mane Six found and eventually returned them to the tree meaning that some of their essence has now become part of the tree. Meaning anything from all of them becoming immortal alicorns.