1. The voice is the Fate computer. She is most likely directing that towards humanity as a whole, since she is programmed to protect them. Fate is a complex computer who might be able to emulate emotions (maybe). So what she means that she loves humans, and that she has to destroy them sometimes to protect them as a whole. Which is why she eliminates dangerous people that threaten to ruin the careful balance she created like General Viper.
2. Miguel seems to have resignated himself to Fate's wisdom, and might have even agreed with her to a certain extent. Seeing it as a necessary evil. She was manipulative, but in the end she was keeping the balance necessary to protect humans, which the planet saw as a pest. Though brainwashing is not past Fate, since she eroded Wazuki's soul away...
3. Fate wanted the flame for power. The power to continue to keep things in control, like protecting humans from themselves and from the Dragon Entity. Protecting the flame was also part of Fate's programing, and it was even hinted that Fate wanted to become a new life form with the use of the flame. This is further reinforced when she asks Serge to teach her what it truly is to be alive. A sort of jealousy and desire for life.
4. Zeality covered this pretty well. The Dragon Gods were actually far gone, consumed in the distant past. They were a part of Lavos or maybe even one of the Lavos Spawn, but it gets too confusing from there. Their will still exists, which was strong enough to make that projection into the physical world. Lavos/Schala might have also used this to gain access to the physical world like Fate with with Wazuki/Lynx. Remember, he's stuck in the abyss.
