The Bionis and Mechonis are standing in an infinitely large ocean. The sun still rises and sets. Where does the sun go at night?
Looking at the sunset from an open area, like the Fallen Hand, reveals that the sun doesn't go down the horizon, it vanishes before reaching it. One of the heart-to-hearts reveals that the "stars" in the night sky are actually just ether; who's to say the Sun and the Moon aren't just ether that looks like the real deal too? This would especially make sense when the true nature of Zanza and Meyneth is taken into account. They made it so day and night looked like what it was back on Earth, but without the "other celestial bodies out there" part.
Why do the Machina have breasts? And why do theybounce? What sort of metal does that?
Because they're beings made in the image of a human, and humans have breasts.