It's a good question which will lead you to some very interesting territory. This concept is not to be taken in a straightforward way. It is, after all, appearing in Midrash. Like most things in Midrash, it is alluding to a different concept. The allegory only gives a simple model to make it possible to comprehend a much more complex concept.
For an excellent discussion of this subject and what the concept is about these 3000 allegories, you should try learning this Chassidic Discourse of the Lubavitcher Rebbe entitled, "להבין ענין תחיית המתים". In particular chapter 6, which appears on page 225, is explaining the concept and pointing to additional explanatory sources. Happy learning!