About the option, I marked this as a bug and will take of it soon.
Actually many plugins rename the files without modifying any posts or anything else. They do this and only this. The reason si that modifying all the posts, pages, metadata is very tricky: depending on your install and the plugins you are using it is virtually impossible to cover all the cases. When I did this plugin I knew I would play with fire (this is why here are warnings everywhere) but I wanted to give it a try, make it work for my basic installs and common plugins and it works. Now I am trying to improve it but it will never be perfect, that’s impossible. However, not many attempted to make a similar plugin. To be honest, now, when I am making a new app or plugin, I prefer to stay on the safe side – less issues, more happy and positive reviews. I have another “dangerous” plugin on the repository called “File Media Cleaner”, that one is a real challenge as well.