We’ve been over this before, the ponies always had access to the magic
Already in the movie it was discovered that the magic in Equestria/Equus is layered, the unity crystals block active pony magic from the ponies that can normally generate this - but this does not affect the internal and “inactive” magic that gives the ponies grip ability, cutie marks and creation of magical mana/essence in them. Chimeric creatures and creatures with appendages such as horns and wings have been able to exist by having internal magic. The ponies are slightly different from the other species in Equus in that they have externally active magic and are more “magically active” than the others with few exceptions.
The new information about the dragons revealed that this principle of external active magic and internal magic not being touched also applies to non-ponies. When Opaline stole the Dragon Stone, she was able to tap out dragon magic in addition to stealing fire magic. She couldn’t use it until she got hold of a dragon, that explains why Sparky was so important, he was the “key” to “open” the channel into the dragon magic. She uses the same method by stealing cutie marks and integrating them into her together tree, to drain the magic from them, and the unity crystals themselves.
But the internal magic of all living creatures in a magical world could not be stolen. Think it’s soul binding magic related to instincts and basic emotions, emotional magic seemed to be very important because it can’t be destroyed. It could explain why ponies and others become so emaciated and near death when the changelings sucked too much out of them. Emotions are magic in Equus, and friendship is magic. In comparison, other magic is more artificially based and easy to steal.
Magic can be stored in crystals and inorganic objects such as amulets and lockets, but perhaps it works like electricity in our world, with a “transformer” from an organic life form to an inorganic object. Tirek and Opaline couldn’t take magic from them. With this ulterior motive then it becomes easy to understand why Twilight came up with this idea of making magic impossible to steal. But Opaline found the solution by growing a together tree that can transform magic and makes this available to her. And when she took the cutie marks, she could just put them into the tree for the same purpose. The tree was her key.
Early on, she had likely only been able to steal magic from the dragons by utilizing her elemental talent linked to her cutie mark, and that made her so formidable, Twilight probably had her hardest fight when she confronted and defeated Opaline. We don’t know how much Twilight and her friends had to pay to defeat Opaline who may have drained fire magic from many dragons. Judging by Spike’s reactions, a lot. And since Opaline could take cutie marks with her spell, she had been able to use the same ability as Tirek.
Basically, Twilight had been very thoughtful, but unfortunately she hadn’t anticipated that the three crystals would be separated from each other for too long (perhaps a time limit of several months or a moon/year) and that Opaline could be solution-oriented in addition to her cunning. As the magic disappeared - and then returned - the plan, as the dragons mentioned, began to fall apart.