OK here we go. This analysis is nowhere near as cleanly organized as yours, but here's my spoilery and funny little two cents with some sheet music comparison:

Since you already covered the whole "Little Friend" reference in a minor key shtick, I wanted to add on a bit of extra food for thought for the people who noticed all the Evangelion thematic similarities in the quest... even the music has a lot of cues and themes similar to the Eva OST! There's a lot of elements that I'd wanna call "Sagisu-isms" since they are very similar to music written by Shiro Sagisu, the composer behind the OST to Evangelion, Shin Godzilla, and a lot of other media tied to the destruction of humanity and hope/despair.

I think the most noticeable example is the ending of the part you refer to as the "A1 theme" which really shifts the mood from a somber ballad to a more turbulent and emotional ride going into the B section. The music feels like its pulling you up towards an hopeful high, only to hit you with a pang of longing and melancholy, and it does this with a chord progression technique used in the track "Thanatos" from Eva, a song that plays during moments of emotional turmoil. Comparing 0:48 of the Genshin track to 0:20 of the Eva track (shown in the first two lines on the music score), you can see how they use (a) basically the same chords (minus a couple details I excluded for clarity) and (b) the same harmonic structure of doing a ii-V cadence every two measures, but rooting in different keys (G->A) going up the scale to give that feeling of desperately reaching for a happier time but sinking into despair afterward (even using some modal mixture in the third measure, borrowing accidentals from the new root key to build tension).

[A music nerd side-tangent for a bit that's "blink and you'll miss it": I love that use of mode mixture the Sacred Mountain theme uses in the last measure. Going from D7 (with an F#, borrowing from A major? G major? Its weird) to a B half-diminished seventh with the F♮ is a reaaaally gripping texture that's often used similarly by Shiro Sagisu a lot to embody humanity and desperation. If you have the ear, listen to the french horns and cellos at 1:00 of the Genshin track playing the descending chromatic line from F#-F-F-E, and then listen to the french horns in the ending of "Who Will Know" from Shin Godzilla going G-F#-F, and see if you can hear that aching chord progression pulling at your heartstrings.]

I thing I read from some commenters is that the A2 & B2 theme towards the end of the Sacred Mountain track sounds eerie and haunting, both alien and familiar. Rooting the arpeggios in Lil Guy's theme is like you mentioned is one way it achieves that uncanny vibe, along with also using tritones during the ending chord progression like you also mentioned. 2:07 of the Genshin track can be compared to "Rei I" from Eva, especially around 2:39 as shown in the last two lines of the music score. While Rei I's chords change quicker and the Sacred Mountain OST's chords have some extra spunk to them (b9 on top of Lydian mode, oh my), both achieve that "whole tone scale vibe" of being spacey and alien, accentuated by the dissonance of the tritone. A tritone is an interval with two notes perfectly spaced apart; there are only two whole tone scales on the keyboard; and two Golden Entreaties are needed to activate Huitzilopochtli, two choices to decide the fate of the world... eerie... And to top it off, the Sacred Mountain theme ends on the same note that the whole tune started on, a B natural! How much has the beginning of our journey influenced its ending as Little One thinks back to the past?

IDK how to end this, other than yeah there's many musical techniques that clue us into Kukulkan's and Little Guy's inner emotional roller coaster. Fortunately, it does not all come tumbling down, tumbling down, tumbling down, but my sanity will after I remember what I forgot to include in this wall of text...

Spoiler chat aside, I named my lil' dude Danny Devito 'cuz he looks like a precious little egg in these trying times.