Assuming that the format used for existing user data can be converted to the current format via automatic lightweight migration, it doesn't matter that you created internal, unreleased versions.
What you need to include in the released app: every version that any user might be using. In your case it looks like people would only have 1.0-formatted stores, so there's no need to include 1.1 or 1.2. If that's not the case-- i.e. if there's a user out there somewhere who might have version 1.1 or 1.2 data-- then you need to include them.
So, as long as the 1.0 --> 1.3 changes work with automatic lightweight migration and that no users have 1.1 or 1.2 format data, you could just delete the intermediate versions.