The Windows bash shell would be a lot better if you could interact with files on your normal Windows filesystem, like Desktop and Dropbox, and vice versa with opening files you made in Bash in Atom outside.
With WSL, I've been able to run Linux-based dev and build tools and Windows IDEs at the same time on source stored in the Windows world with no issues.
On the other hand, it's true that you can't / shouldn't modify files on the Linux file system (i.e. Files outside of /mnt/...) in Windows itself since the Linux-specific concepts would get mangled. With the mounts though, there shouldn't be any need to do this.