I'm not a KA guardian, but I have been using the KA CS platform for a while and played around with webpages and b64 file encoding. 

I would say the program you linked to does violate the guidelines. Of course, that's just my impression, don't take it for anything near certainty. Here are my reasons for that:

The guidelines regarding sound read,

Webpages should only create sounds using the files available to ProcessingJS programs or the Web Audio API oscillator. Webpages should also only play sounds in response to user interaction. Webpages should not play sounds immediately upon load.

If you try use an audio file the standard way, by linking to an external audio file, Khan Academy will block that url, not allowing you to play media on external servers for security reasons. The program you linked to gets around this by encoding the audio file into a base64 url before playing it, basically storing all of the audio file's data in the url itself instead of linking externally. I've tried using b64 urls before for other files, like fonts not available on Google Fonts, or basic images and icons, and KA has blocked those from working, as noted when I checked my browser console for errors. It only makes sense that KA would need to regulate b64 urls as well, as a user can encode practically any media file into a b64 url, provided it's small enough, and that defeats the purpose of controlling what media is shared on the platform.

This user seems to have gotten around this regulation with some clever JavaScript, but I'm afraid that doesn't make it legal.

Going back to the regulations, is it one of the files available to PJS programs? No, it's an HTML program. Is it one of the Web Audio API oscillator sounds? Absolutely not. The Web Audio API oscillator is a tool to produce sound programmatically with primitive oscillators, not a way to play b64 encoded audio files.

In conclusion, let's wait for a guardian to give the final verdict, but I don't believe using base64 encoding to upload arbitrary media is permitted by the guidelines, and I wouldn't risk trying it until you get explicit permission.

Hope that helps a bit! :)

Hi Nicholas, thank you for your answer. I really apologize for the late response.
Your answer really makes a lot of sense and I thought the same thing as you when I first saw the program. What I find weird though is that that program has a high amount of votes, and the program has not been taken down. On top of that, the creator has claimed in the comments that his code script was allowed by a guardian, and people seem to believe him.
I'll hope a guardian answers this soon, but thanks for putting a lot of effort into your response!

I'm not speaking for everyone, but:

I believe in the past we've allowed it in good faith, so long as you only use appropriate, relevant, non-copyrighted works. I personally think it's that way at least partially because it's not the simplest thing to learn how to set up, so few users know how to do it.

There are several other programs of "music players" that use base64 encoded data, whether directly in the program or loaded from jsdelivr, and I don't think they've been hidden either.