There are some small differences.
The version from my store will give you exactly 2 more options during setup for enhanced removal of Safari History and Cache.
With a little extra effort, you can make the App Store version function just like the trial version.
First of all, you will need to download and manually install:
you can find the link with more info about how to install the script here: https://sweetpproductions.com/products/cookieapp/scripts/en.htm
Basically you need this script if you want to fully remove Safari search history.
Run the following command in Applications/Utilities/Terminal.app to enable a deeper clearing of Safari's cache:
To run the command, you only need to open Terminal.app, copy and paste the above command, then press ENTER.