Your "Physical folders" settings is a little confusing and suppose don't really needs on clear WP install when no any media or additional plugin exist? Please, add to your plugin "Physical folders" section and to documentation: https://www.joomunited.com/wordpress-documentation/wp-media-folder/584-wp-media-folder-physical-folders
- info of which options can be disabled on WP clear install and when NO any 3-rd party plugins which works with media is present.
Suppose options "Search into full database" and "Replace relative paths" - can be disabled?
What about "Detect media tables to replace content" option? It really needs? Maybe can bee set to just 1 table-column where WP store media paths? Or default place will be replaced with "Physical folder" on media upload anyway so this option can be disabled also?
PS It seems that your support team don't know what those options do.