Manually setting backup points - alternatives to Time Machine
Because of the way TimeMachine has saved the data, you don't actually have two copies.  It just seems that each backup is a full set of files (which it is; but, in the background there is some nifty unix filesystem "trickery" going on).

If you go to the enclosing folder (π's MacBook Air) or the top-level of the hard drive itself, you should see around 22GB used there, and not 44GB.

(Edit)
As for dragging/dropping, unless you do it as the root user, some files will not be copied into your destination folder, due to permission issues.  And, copying large amounts of data via Finder can strain your CPU and your patience.

Rsync is a better alternative than drag/drop.  And, if your goal is to set a bookmark for your file system to revert to after experimenting with text editors and what-not, it might actually be better than Time Machine.  Time Machine is good for recovering accidentally deleted files; but, if you want to return the computer to a previous state, you would have to "restore" the complete old Applications/ folder, just to "remove" the new files added there that you don't want anymore.  Rsync would make that a little more amenable.