Well you could always test it, but there does look to be something wrong. Perhaps nothing that will break it, but duplicates that are redundant and could pose a conflict issue.
Since you have a retail game, I believe all the assets are installed into the redist folder - nothing much in the root folder for Amnesia. Like so:
So seeing as you have loads of files in your root, that seems to be incorrect. For Steam copies, all files are in the Amnesia root, but for retail, most files are in the redist folder.
Basically you should have a similar setup before you start installing the update. These files are extracted by the 1.3 installer.
Therefore these files and folders should merge with your install and leave you with something like this
>root
---->Amnesia.exe
---->Launcher.exe
---->redist
|
---->config
---->maps
---->entities
etc
I'm quite certain you can delete the 1.3_update folder after install.
Of course once all this is done you can throw in the 1.3 editors in your redist folder.