itch.io

If you mean the different pitches for the sound effects, each part of the music has a different chord note assigned to it and that note is used to determine the pitch the sound effect is played at.  (This is a thing I've also used in a previous game, though it's more noticeable here due to sound effects playing more often.)

All the audio is synthesized during the game, and I wrote the code to do that (a lot of that code is part of the "non-game-specific stuff I copied from other games", and ultimately it uses JavaScript's Web Audio API), so I can make the format that I made to store the music have a way to specify a chord note.  When the code reaches that point in the tune, it stores the frequency of that note in a variable.  The sound effects are entirely made using code, so they can calculate the frequency to use based on that variable.

It would also be possible to do this with sampled audio; you'd need some way to store a list of time ranges and which chords they go with (e.g. 0-1 second, C major; 1-1.5 seconds, G major; etc.) and then either choose different sound effects or change the pitch of the sound effect based on the current chord.  There might be tools to make that easier; I don't know, since I haven't really looked into it.

There are also specific points specified where tunes change to other tunes.  There's a four-bar intro at the beginning, which loops until you touch a platform for the first time, and then when you win it switches to the ending theme, and both of those wait until the end of a phrase.