@Trickquestion
I don’t think the Element of Magic “worked by itself.” The counterparts of Rainbow Dash, Fluttershy, Pinkie Pie, Rarity, and Applejack, and given how they’re basically identical to their pony counterparts, they’d have the same respective traits represented by the Elements.
So basically, while the physical Elements or their bearers may not have been present, the Element of Magic could somehow draw from the Loyalty, Kindness, Laughter, Generosity, and Honesty in the same way.
It’s sort of like what happened at the end of Digimon Adventure. Apocalymon shatters the Crests and banishes the Digi-Destined to the binary code of the Digital World, where they’re unable to do anything except reflect on their adventure and what they’ve learned.
It’s then that they discover that the Crests themselves were actually powerless: they merely drew power from their bearers’ virtues and acted as a focus for it. Thanks to their experiences, they’ve strengthened their virtues to the point where they no longer
need the Crests to draw power from the virtues they represent, and use that power to escape from imprisonment and defeat Apocalymon.
Given that the Element of Magic is the only Element that doesn’t represent some sort of virtue, and given that it was summoned by the presence of the other Elements, I believe that Magic is the one that actually does the work: it draws power from the virtues of the other Elements and converts it into a usable form.