Maybe a simpler explanation to what you meant to do could help you understand the concept of the process.
Your console NAND has bad blocks, that's how it was programmed and came from the factory.
When you create an XBR or Freeboot image to replace your original NAND the bad blocks get rearranged and as of a result when your console try to look for the bad blocks in the area they meant to be it doesn't find them and hence it gives you the error messages you were getting.
By remapping the blocks, you are placing the blocks where they meant to be originally.
Once you created your XBR or Freeboot image, you are meant to extract those particular blocks and write them back to the image at the locations originally they were on the original NAND.
Does this make sense to you? If it does, it should help you understand easily what you are meant to do by following the guide.
