".fts" is the "FME Feature Table" store. This is a more compact, faster way we deal with data that is known to share a schema across rows. The File Geodatabase (API) reader was an early convert to this new method of handling data. So I'm not surprised you saw what you're seeing. And the .fts does carry by far the bulk of the data, so that is why there is the size difference.
Right now CSV and MapInfo Extended are the other two readers that work in this way and would result in .fts files when written to FFS. An increasing # of transformers are being changed to either work upon or output data using this new technique, but all any user should notice is that things just work faster.