Re: So, exactly...
The concept is actually very simple. "Everything as a file" means that you can use any tool you like that works with files on other things. It's incredibly powerful.
An analogy to what was happening here could be like files in a remote share in Windows that appears on the windows desktop. It looks like folder containing files, but is not stored on any hard disk local to the system, and does not actually appear in the user's "Desktop" folder. It's abstracted to a different storage medium by the OS, so wiping the local disk by formatting it will not touch these files (in this case, on the share). Like psuedo filesystems in /sys, files on a share can be explicitly overwritten or deleted, but formatting the disk won't touch them.
For a share, the files are actually stored on another computer. For the /sys directory on Linux, it is 'stored' (or translated) to another medium than the disk, which can include the NVRAM in UEFI. Some entities in /sys are read-only (mainly for providing information, but also for input only devices like keyboards and mice), but anything that can change will probably be writable with the appropriate permissions. Being able to write to UEFI allows Linux utilities to make useful changes to the way the system boots the OS, amongst other things.
Like everything UNIXy, you should treat super-user (root) with more care, and you should never really do more than is actually essential with raised privileges.