Those are good points.
To test this time travel theory further, I went back and rewatched some scenes from Episodes 1 and 3, specifically Homura's first conversation with Madoka, Homura's first confrontation with Mami, and Homura's scenes in Episode 3.
A few things stood out to me while doing so:
1. Homura is clearly already very familiar with the overall layout of Madoka's school. She knows exactly where to go to find the nurse's office, which Madoka found odd herself. She also already knows Madoka's name, and even Madoka's role as Class Monitor. This all makes sense, of course, if Homura is future Madoka.
2. Homura notably grimaces when Madoka talked about how unusual but cool Homura's name is. That could be due to how Madoka saying that is a painful reminder to Homura of when she chose to be a magical girl, and why she choose Homura as her magical girl name...
3. Homura doing exceptionally well in school could be because she's done all this school work before.
4. Homura notably grimaces a bit during some of her meetings with Mami. Perhaps this is because it's killing Homura to have to be this confrontational with Mami, as she liked Mami a lot and promised to remember her.
5. ... Homura doesn't look a lot like Madoka, but she
does look a fair bit like Madoka's mother (she even has the same eye color as Madoka's mother). Homura's hairstyle is also like a longer version of that of Madoka's mother. Perhaps Homura's appearance resulted in future Madoka wanting to be a magical girl that looked like her admired and beloved mother.
The more I think about it, the more this theory really does seem to fit very,
very well...