I am also having this issue. All strings are LocalizedStringResource and the catalog correctly has all the English translations. However an en.lproj folder is not create when archived.

I found a fix. You can right click an entry in the catalog and select "Mark as Reviewed" and it will then create an en.lproj folder and file. In source code view you can bulk edit "state" : "new" to "state" : "translated" for all English values. On build it will also then remove "extractionState" : "extracted_with_value" from each entry and all strings will be in the en.lprog strings file.