The former condition just checks if a package has been flagged as containing some kind of data of interest to gathering for localization. The latter condition is an old fail-safe so that packages that were created (and not yet resaved) before we added the flagging could still be processed anyways, just in case.
That still strikes me as very unusual - it changes based on what directory you place the file in, which shouldn’t affect whether the flag. The flag is set when a localizable FText object is serialized into a package.
It’s going to be difficult to track this down short of having a zipped up project with the reproducible issue. Without that, my best tips are to try loading and saving a single UObjective asset in the editor and see why the flag is getting set from FText’s serialization methods. If it is, then why it isn’t set when the package actually serializes to file on disk or when loaded from file on disk.