if you really like to have 1 to 1 the same it's better to copy the disk than to use Time Machine. With time machine it works like this at first it does a proper new os install the copies the files from these Folders back to your disk.
so if you use something like homebrew, macports or fink or any other terminal tools witch install them selves in /usr/local/bin they will be lost.
Also things like changes made by lion tweaks
and candybar etc. will be lost.
Also self made permission changes on System folders or icon changes on these folders may get lost.
For a 1 to 1 copy you can use a os x install usb stick or any live linux stick with gparted on it.
then clone the whole disk (including the hidden restore partition).
now boot into the new disks restore partition and run a disk permission verify/repair and if needed also a disk verify/repair so you know your os on the new disk works all fine.