You can extract everything and upload the folder instead of uploading a single file. You can easily do that regardless of if you're using QuickTorrentMaker or creating your torrent manually from within your client.

It's safer that way and people get to know that's actually inside the game folder.

If you think there's any additional steps to manage to play the game you can just add that to your torrent description.

technically, you are not supposed to upload RAR files, but in the case of binaries, that is often done.

Nothing against it in the rules. They simply say not to upload video packed in archives, so all good in this case.

There are many ways to rename a file. Try using file explorer (or whatever it is that you are using to locate the file on your hard drive) and right-click on it.
you could also use the CMD command, and use CD\ and CD whatever to navigate to the file.. and then type MOVE filename.rar filename.new or RENAME filename.rar filename.new

or unzip the file package a bit more simple
and post entire folder and files in one directory ...

• Do not upload VIDEO packed in archives (zip, rar, ...), password protected files,
  or material that needs to acquire a license for playing

However you can change or rename .zip, .rar
ex. xxx**.rename** [xxx**.zip**] ...
and make a note from the origin file name to avoid confusion ...