I can't clone (Duplicate) my Time Machine backup properly via Disk Utility

I have an ext. HDD Time Machine backup sitting beside my 10.8 MBP.

I want to create an identical ext. HDD Time Machine backup, because it's safe to have 2 identical HDDs backing up my system.

But when I follow this apple guideline, a problem occurs:

Time Machine: How to transfer backups from the current backup drive to a new backup drive

URL: http://support.apple.com/kb/ht5096

The problem is I get a strange path even if I drop "Backups.backupdb" of 3TB1 (The source HDD) onto the root level of 3TB2, the destination HDD (I mean there's nothing in there so I just drag & drop onto the HDD). And the result is my new ext. HDD eating up about 60GB more space.

I have attached pictures of the paths for both Source HDD and Destination HDD, please look.

Why does it alter my file hiearchy like this?

Please help some high-level Mac guy thanks!