Installing a program like Wordpress manually is not particularly difficult if you know how to do so. You will need to take steps such as creating the database, database user, uploading the files, and manually editing the configuration file. All in all, you can get that done in about 10 minutes.
Using the Softaculous installer, it takes only a moment and does all of those tasks behind the scene.
There is no security difference between the two as you are able to change the database name, table name prefix, select your admin username and password all from the installation form.
The only thing the manual install has control over that the auto install does not is which version you install. Softaculous uses the latest version, which is typically advised.
Overall, it is largely a personal preference. As someone who has done both many times, however, I side with the autoinstaller.
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