Yes.
To be honest, the separate plugin config folder could’ve been avoided. I made it because it allows for managing of the config files (if the plugin gets deleted, you can choose to keep or delete the config files, for now it always deletes them. If I put them in my plugin folder, WordPress doesn’t allow for preserving config files when a plugin gets deleted).
In the future I might make an update to move all the config options to the database. For now I haven’t done this yet because on my web server there is a minimal increase in page load time if I do.
As far as I know, storing my config files in a separate folder doesn’t really have a disadvantage over storing them in the same folder, except that the plugin has to remove the files and folder upon deletion, which mine does, and there are no security risks in it. I don’t really see why your security plugin marks this as an issue. Obviously, if I was allowing for PHP code to be written in my config files, it might be a different case, and maybe the security plugin can’t differentiate.