Why does Font Book duplicate some font files in my fonts folder when activating the font? I end up with two separate font files.

Do you mean something like this?

Greta

Greta Italic

Instead of just Greta at the left and your style choices at the right?

If so, that's caused by the internal names of the fonts. Instead of the fonts having a common Family name of Greta, the creator gave each font a family name with the full name of the style. By doing that, they list as separate font families instead of being grouped together.

Hard to say why it's doing that, but the usual fix when Font Book starts doing anything wonky is to reset its database.

Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. You can let go of the Shift key at that point.

OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally. This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode.