I get that Madoka would have to be a fundamental law of the universe considering that she's overwriting the concepts that the universe is based upon, but her only wish was that to erase all witches before their creation. However, somehow, Madoka now suddenly knows everything about the universe, including how Homura worked hard to save Madoka throughout all those different timelines. How does she have access to that information? How was she given vision of the entire universe and all events within if her wish didn't reach that far? She only had one goal and that's all she wished for, but she was given sight of the whole universe.
It's because it was told to her in Episode 11.
Madoka visits Homura's house, where she asks her if it is really not possible to defeat Walpurgis Night alone, as Kyoko said. Homura denies Kyoko's words, but Madoka finds it difficult to believe her. Homura then reveals her true identity and history to Madoka, hugging her.
you can also see a transcript of their conversation on that page aswell.
Later on in the episode Madoka leaves the shelter to talk to Kyubey who tells her that Homura fights because she has hope and if the worst case scenario occurs Homura can go back in time again. this more or less confirms to Madoka what Homura has gone though proably already assuming then Homura's been though a lot due to how she acted when they were together at Homura's Place
Also remember that at the very beginning of the series Madoka had a dream of the a timeline and it's confirmed later when she meets Homura. one can assume that Madoka has the knowledge/memories of all the previous timelines inside her has her karmic destiny builds up but probably not understanding what they mean at least until she learns about who Homura is
Also her wish did reach all of the universe as her wish was
to erase all witches from existence before they're even born. Every witch in the universe, from the past and the future, with my own hands
which means she is everywhere in the universe from past to future. you could consider the alternate timelines Homura terminates as apart of the universe given it is all these timelines that Madoka got her god like power from (as originally she was a normal Magical Girl)
However if you interrupt the "everything" Madoka knows as being more than her and Homura's fates then you need to know how Madoka seeks out Witches. My assumption is that there isn't another system or force guiding her rather Madoka exists in every moment in history all over the universe observing and waiting for a witch to appear.
also her perspective of time will no longer be linear like everyone else such as when 2 Magical Girls become witches, she must exist in both places at the same time to ensure that there is no chance a Magical Girl becomes a witch as her wish is to erase Witches before they are born