Files end up in the Fonts folder if they have a "ttf" or "otf" extension. Make an issue on the tracker for "ttc" files.
But even if your TrueType Collection files end up in the Misc folder, you can still use them just fine. There's no semantic value in the folder names, they're just a way to organize files.
So just reference the file from the Misc folder. And yes, you have to change the CSS to use the font. That's how it works for epub.