is_substat isn't used in Stats.*, but it is used in TreasureTable.*, ItemProgression.*, etc. For example, ST_StaffNormal in TreasureTable has three substats.
Also, in case you had not figured this out, I forgot to mention you have to edit the .stats file in the Stats Editor, save, revert your change, and save again in order to generate the corresponding .txt file. "Save All," unfortunately, does not rebuild all .txt files. It should, but it doesn't.
By the way, I'm working on a CLI enhancement for the ConverterApp that can be plugged into scripts, and I think Norbyte is working on a STATS-to-TXT converter. Together, these will allow us to generate data mods by script without requiring the editor for anything except publishing to Steam.