From what I know about this great plugin, having different options of security caters to all users needs.
Remember you probably won't be able to enable all the security features in the plugins for various reasons and if you try to without thorough testing you might lock yourself out of your site. It has happened to many. That is why the developers have gone to extra lengths to add lots of instructions for everyone to read before they enable and implement an option.
I don't enable this security feature in the plugin for my websites instead I use Google Authenticator and this plugin, which gives me the level of security I am happy with.
However my setup might not work for everyone hence the reason why there are many security options available for you to choose from.
I hope this helps you further. If you need more help let me know.