Where Softaculous - for the end user - has "Advanced Options" for the "install" available for updates and backups, are these always only referring to having Softaculous itself perform these features?
For example, for Wordpress, the description is clear that the backup option here refers to Softaculous making backups, and is not related to any WP built-in option to make backups. But the options for updates are unclear (to me) as to whether it is configuring Softaculous to perform updates automatically ---OR--- is it going ahead and configuring some basic options within WP's own functionality for you as it installs?
It is important that user's should be aware that in most cases, they should probably only CHOOSE ONE of Softaculous or WP or a plugin to handle such features and not enable duplicate/conflicts.