This is a UAT-driven workflow in the editor that's not currently looking at the INI setting to infer whether or not -nativizeAssets should be implicitly added to the BuildCookRun command line. It should probably behave the same as File->Package Project, which does implicitly add it if the value of the INI setting is not set to "Disabled."
BuildCookRun.DoBuildCookRun: WARNING: Project is configured for Blueprint nativization, but the conversion flag (-nativizeAssets) was omitted from the command line. No nativized assets have been built as a result.
Head over to the existing Questions & Answers thread and let us know what's up.