Amy supposedly read in some Tarot cards that she had a 'destined' encounter with Sonic on Little Planet, but then I guess that's more accurately 'why', as for how...she climbed the chain?
When Sonic sees the Little Planet, it's covered in metal. I would think that the Past and Good Future would have the sky visible, but in the Present it is even before the generator in the past is destroyed, and why is it visible in the Bad Future at all?
Possibly Gameplay and Story Segregation for the most part, but for some stages, that can be explained away as Sonic standing on top of the metal the Little Planet is covered in. However, the D.A. Garden shows Little Planet in all it's glory (or lack thereof) and there's little to no metal covering the place at all. The metal covering was only shown in the full-motion videos. Knowing what we know about the stages themselves, the D.A. Garden rendering of Little Planet might be the more accurate depiction of the place.
You could be right. The D.A. Garden is probably what it actually looks like and I'd imagine the version of it covered in metal was from concept art or something.
What is Metal Sonic doing in those projectors?
It looks like MS is tormenting them. My thought is that those projectors were built to scare off the animals, hence why you see them prancing around in the level once it's destroyed.
Why the hell is that "Fun is infinite" easter egg in a Sonic game?!
Someone in development probably threw that in as a joke.