I think if you read Swen's latest blog post you'll get an idea of why it's both really. They started out making a big patch with some content changes but it grew to the point of touching core game and quest mechanics such that it was no longer compatible with the original. You can't release a patch that breaks your saved games, so it's coming out as an EE. It sounds like it will certainly fit the designation. I don't see any duplicity, just something that was evolutionary.

DOS2 Mods: Happily Emmie After and The Noisy Crypt

Steam Workshop
Nexus Mods