Why is there a train station in the middle of the jungle?
It's a video game.
That's not an answer. Come on. Try to think about it. Maybe the jungle is a tourist spot?
Archeologists use the train to commute between Station Square and the Mystic Ruins. It was probably integrated into Station Square for the sake of being a tourist destination.
How did Birdie get a locket with a picture with his family in it, much less one with a Chaos Emerald? Did he purchase it? How can he even lift it?
It is a video game.
See above third tier bullet point.
It's been shown that all animals in the Sonic World are higher functioning than what would be expected of normal animals. Birdie's family probably got the locket and took a family picture to put inside it just like any human or anthro would. As for the Chaos Emerald inside...*Le-Shrug*
The Chaos Emerald is a shiny object, birds like shinies, and the Chaos Emeralds are hidden across the "world" anyway. The three birds find it, keep it, and then two of them get kidnapped by Eggman and the other one gets chased by Zero until it runs into Amy.
Could Sonic have reached the last Chaos Emerald before Chaos if Tikal hadn't stopped him with that final vision?
Given how often Sonic lost the chaos emeralds every time by some contrivance, then no. Vision or not, Sonic or somebody in the game would've lost it to Chaos anyway.
Is Tikal sending the heroes back in time? Did those brief moments when they interacted with Tikal in the past actually happen?
It is either inconsistent writing, or some characters were sent into the past (Tails) while others only received images (Gamma)
Actually, at one point, Tails mentions that Sonic apparently was "out of it" during his visit. Course, it might mean that they'd have to have seen him standing there with a blank look while his mind was literally in the past.
Tikal's sending them back in time mentally, with their mental selves temporary manifesting a new body. Their original body goes into some sort of trance while this happens.
If that is the altar for the Master Emerald, then what is the Hidden Palace Zone?
Well given the name it's probably a place where the guardian hides the Master Emerald when they know their is danger.
Still counts as invoking the Chaos Architecture trope, since it was not confirmed that they're different locations within the game, nor that they're the same, for that matter.
Regarding the Inferred Holocaust: Really, none of the characters give a shit about an entire metropolis destroyed and its population presumably killed? "All's well that ends well", Tails? What?!
I guess he felt that it could have been so much worse.
The people could have all escaped. It's not like we see any waterlogged carcasses floating about.
In the Sonic X anime, the following episode after the Perfect Chaos battle has the citizens fixing it up.
Eggman's goal. He didn't seem to think his plan too well. His plan in this game is to create the ultimate city over the ruins of Station Square. The...flooded ruins, that is. If his plan was to build a city over a flooded land mass, why not just build it in the middle of the ocean somewhere? And who other than Sonic does he expect to come to this city knowing that he just rendered countless people homeless in this act? And why need Chaos when he has his own military might? He's got a flagship, countless war machines and even a nuke at his disposal to do away with Station Square at any time and Chaos himself fails to defeat Sonic, Tails and Knuckles despite having the Emeralds to himself. But I guess my real gripe is: You've got an almighty morphing god of destruction entirely composed of a mixture of infinite energy and your archenemy's greatest weakness who grows stronger with each gem of infinite power you feed him. Why would you waste all of that on destroying a city just to make an apparently better on over it when you could hold the entire world under threat of global flood?