Hints: In chapter 65 Negi and Nagi Springfiels showed with Mage of the Beginning too. Chapter 84 in Touta's training he obtain the power same with Negi Springfield but here is the other thing.
How Touta Konoe possess the white Angel power. His master told him that he has two powers that's why he can't use magic in the same time but only strengthen his strength.
Also, in the brief case of Yukihime's past she was thought the first subject of Mage for knowing the knowledge of immortality.
However, the Mage of the Beginning shows interest with Touta in that scene. But it seems you may compare his image to Touta's appearance (old version).
In the scientific explanation, clones has no soul nor spirit, maybe they have a power from the original but they are mere a puppet or a doll (it has being said in chapters between 82-90). Touta admits he is just a tool to be use inorder to kill the Mage.
Another thing, the Mage of the Beginning has another experiment 800 years ago before the event of helping releasing Yukihime from the seal in Magister Negi Sensei. Maybe it is the homuculus project where the Mage used his own power to create a weapon that can destroy him but it was not yet completed because there is no one in his time possessed a power same as he. Then 780 years later where Negi fought him. He kidnap both of them and used them to complete this homunculus. Then the result is Touta with no memories.
However, 2065 inorder to save the humanity he used his powers to defeat him and have an agreement. The Konoe family discovers the labyrinth where Touta's bodies is inside. Then 20 years later he is ready to be awake but then Fate get angry and killed all of them including the foster parents.
Now let see is Touta is a mere clone or an empty vessel ready to be possessed as the new body of the undying Mage of the beginning.