[color=red]SPOILER ALERT
SPOILER ALERT
SPOILER ALERT[/color]
I just realized something. Homura always thinks she’s more powerful than her opponent: it’s her greatest weakness. It’s how Kyubey repeatedly beat her in the first stable universe… and how Mami beat her in the second stable universe. Now that Homura has achieved what she believes to be unlimited power, that weakness is still there. Homura also likes to taunt Kyubey, which has always been a massive mistake because Kyubey is really damn smart and finds loopholes in things.
Conclusion: No matter how bad it might seem for him, Homura is gonna get fucked over by Kyubey again in the future. Even with the depiction that Homura is killing Kyubey every time she sees another reincarnation of them, she’s still toying with an Eldritch Horror that can warp reality. For now, maybe not as much as she can, but could find an exploit so long as she thinks she’s invincible.