In principle synthesizing waves is rather easy, if a little obtuse when talking about combining numbers of them, a sine wave is just a sine wave, you take a frequency, and then sample it 44100 times a second, write it to an array and send it to the audio source in Unity, all the other waves work the same, it's just the shapes that are different. As of mixing the waves together, its as easy as adding them together.
I understand the game is hard, hell, I have trouble beating it. I can pass the first 4 levels, then it's downhill for me, and I made this game. That is why I inclyded the "Tip" and "Skip" buttons to help you progress. When you do get to the end, and decode the message, there is a song in the credits which I composed, and a retro style tracker unlocks, which you can use to compose tunes by modulating different waves.
I used it to create the ending song, so I basically created the tools that I used to create the music. I'm rather proud of the result.