So, status update, you still cannot make retail Amiibos with a retail console. When in retail mode, the 3DS will fail to decrypt the Amiibo files included in the SDK. They seem to be encrypted and the 3DS can only decrypt them if it's in developer mode. Of course, once you're in developer mode, it will make a developer Amiibo. This Amiibo can be read as long as your console is in dev mode, but they cannot be read on stock consoles or Wii U. So unless someone can figure out how to decrypt the SDK Amiibo files and re-encrypt them for use in retail mode, then writing Amiibo's with the n3DS will be restricted to use on hacked n3DS.
However, the good news is this does prove that the n3DS can write blank tags, so a homebrew app to do so should be possible.