There's a fallacy here; plenty of intelligent life in the PMMM-verse doesn't have emotions and thus magic. So a non-infinite subset of an infinite amount of lifeforms are capable of performing magic, and a subset of that subset is capable of doing Madoka-level bullshit.
Since Madoka only exists due to the stupidly improbable interaction of literally hundreds of universes, I don't find it even slightly eyebrow-raising that Madoka's the only one to pull this off (well, and Homura, but she's piggybacking).
Also, how do we know that Madoka DIDN'T happen as soon as possible? The Incubators needed to evolve, observe the universe, decide to intervene, INVENT MAGIC (and thus probably are an Omega civilization), and then uplift enough teenage girls until a particular pair with a particular set of personality traits, circumstances, background, and cultural/social mores interacted with each other in such a particular configuration as to cause the start of Homura's loops.
This already requires a stupid number of 1-in-a-few-million dice rolls, but then Homura needs to keep this up for hundreds of loops without A) Dying, B) Witching out, C) Giving up, or D) Succeeding.
And that's not something you resolve with a single probability die roll. You need to make all the rolls in timeline one every single loop, every single time, and Homura needs to pass every single percentile probability every single time.
The fact that this happened even ONCE is retardedly improbable and proves that anything possible is probable.