The opening line: "Proper storyís supposed to start at the beginning. Ainít so simple with this one." Due to the "Groundhog Day" Loop, you're at the beginning of the story. And at the end of the story. And in between loops.
The part where Rucks says The Kid hears a song, asks something to the effect of "How'd that go, again?" and then Build That Wall starts playing actually isn't breaking the fourth wall and makes perfect sense, since it turns out Zia was sitting right in front of him listening to him talk, and the music starting is actually Zia playing the music to Rucks, not her at the campsite.
The final level is Tazal Terminals. Despite long being established as an underground structure, when you get there, the Terminals are overflowing with snow. Why? Well, because the Calamity threw the Terminals up higher than it did anything else! Altitudes!
Zulf's theme (Mother, I'm Here). The song has quite an impact. However, play through the Kid's Who Knows Where. That backstory basically tells the same story as Zulf's theme. Coming home to an empty house, holding his mothers hand only to find out she is no longer with him. This makes the ending where the Kid decides to rescue Zulf all the more poignant. Note the ending song's refrain is "Mother,I'm Here." "We all are born from the Lorn Mother, and in the end, we all return to her." - it's a song about dying and returning to Micia, the "Mother".
It is heavily implied in a New Game+ that restoring the world to before the Calamity sets the world into a "Groundhog Day" Loop, with possibly thousands of iterations. This makes the events and odd narration of the Mushroom Samba episode go from simple survivor's guilt to the Kid's subconscious rebelling against the loop. By resetting the world the kid is literally responsible for that particular Calamity.
The Autosave and inability to go back can lead to some moments of guide dang it but actually helps the theme; Just like Rucks, you do want to replay the game and do better each time and Kid, just like you, is implied to remember a little more each time. Followed to its conclusion, it implies that even if the Calamity keeps on repeating itself, the Kid keeps improving and eventually Rucks' solution might serve as a long term that saves everyone. On the other hand, the player might end up just as shakled by the idea of idea of a hundred percent completion and perfection that they might end up little better than Rucks in the process.
If the Kid is remembers a bit more each iteration, that would handily explain why he's such a Badass at a young age, and a master of so many weapons and skills. He's not resetting things to the time of the Calamity, he's going back years to before his mother died. And failing to save her and Caelondia each and every time.
Rucks' line about squirts getting territorial over cores makes much more sense when you find out they're made of what are essentially millions of squirt eggs.
The Ura are pale because they live in holes, while the Caels are ruddy because they live outdoors.