Linux on Android - viewing file structure
This is due to your CHroot install. The entire Linux hard drive is probably contained inside of a binary file or disk image. 

When you start Linux, you have to use the Android app. It acts like a virtual machine controller. The app mounts the Linux disk image in memory and loads Linux. Linux can never see outside of this sandbox virtual filesystem, and native Android cannot see into it either. Since Android sees it as a single file, ES File Explorer can't view the contents directly (it would see a file named something like Linux_HD.img).

The reason some folders are the similar is because Android OS and Linux OS share a similar codebase. Both Android and Linux (and Mac) have some default folders, such as /mnt, /etc and others. But the naming is purely coincidental for your purpose; changing files within the folder on the virtual Linux install won't modify the Android files.

Depending on the app you use to install and run Linux, it may have an option to mount parts of the Android folder within the Linux file structure.