Madoka was granted one wish and her wish was to erase all witches and that wish was granted. It says it right in one of the scans you posted. All she did was clean the world of witches, she doesn't have complete control over multiple universals. She has universal+ range but that's it. You're trying to hype her up as this nigh omnipotent being who chooses what exists and what doesn't when she only had the power to erase witches which is funny because witches still existed in Madoka Rebellion which was canon. Even if she was a conceptual being that wouldn't matter in the slightest because The In Betweener was a universal, conceptual being and Galactus, who was hungry and just coming out of a coma, fought him and stalemated him.
I don't see what's stopping Galactus from destroying her and Devil Homura together and if we bring the Ultimate Nullifer into this then they both get stomped along with their verse.
Also when was it stated that Devil Homura was stronger than Goddess Madoka? I don't recall her doing anything on her scale or having any hype behind her.
I'm not sure if you looked at all the scans properly. It does confirm that in the scans.
There it says that she wished for the power to remove all witches from the timelines of many universes, and that what she is doing goes beyond messing with time, but rearranging the structure of existance itself. By the way, the full battle of Dr Doom with the Cube vs Galactus ends bad for Galactus.
Pirate site scans removed. -Dream