I see your point. I took a quick look at it again after our conversation. Gives you more guidance on what you can do, but doesn't quite have that same visual picture to keep everything organized. It looks like it uses JavaScript, is that right? I'll have to try it out sometime.
Plus, it probably doesn't help all sorts of companies use Quest as a name. I tried looking up something, using "Quest Engine..." And I got a few company pages.
I think the CSS absolutely destroyed me in mine, so I hear you about the music.
To answer your question, I saw something similar in a few other submissions. When clicking on a word they lead you to a new page to explain what it means, then another button to take you back to your original page, I was looking into it with Twine myself. I think a pop-up would be just as good though too. Players could read the pop-up and close it without any affect to the story. Kind of like this?
If you are feeling fancy though, a hover-over could work as well! I would suggest a journal as well, but I'm not sure if it'll fit into the theme of the game.