Re: So, exactly...
"Are we talking about a situation where the files are actually in the mobo bios, and Linux is making pointers to them"
No. The kernel has access to the mobo hardware and presents them to applications (including rm) through the same mechanism (the same semantics if you want to get technical) as files. Unix lookalikes do this for any hardware resource.
The other thing to realise here is the Unix concept of mounting file systems. The root file system is a disk partition mounted on virtual mount point /. If you have any another disk partitions containing another file system such as your home directories you will need to provide a mount point for it. In the case of your home directory collection you will normally create a directory called home under the top level of your root file system. This is /home. You will then mount your home file system there so it appears as /home. The overall file system thus appears as a set of directories and their files nested within each other and a command such as rf -r will navigate it as a whole. Nevertheless it is still a number of individual disk partitions, each formatted as a separate file system mounted one on another.
The file system-aware tools such as rm are not aware of the underlying partitions. Conversely formatting software is aware of the partitions but not of the mounting arrangements. If you were to re-format your root partition it would not touch your home partition which would simply loose its mount point until you made a new /home directory on the new root partition. This, by the way, is why it's a good idea to set up a Unix-like system with a separate /home file system - you can reinstall the operating system without losing user's data.
Remember that I said hardware resources are made available by the kernel through file system semantics. We need a "file system" where they can be placed. Traditionally this is done through /dev. A virtual file system is mounted on the /dev mount point. Disks, disk partitions, keyboard etc will be "files" here. But such virtual file systems are the manifestation of specific kernel functions and not physical formattable disks they can't be reformatted. More recently kernel resources have also made available through file semantics via another virtual file system under the /sys mount point.
Just as real file systems are not touched by formatting the partition with these mount points neither are the physical items, including the mobo resources, if the root file system is reformatted although, of course, they won't reappear on the reformatted partition until there's a running kernel in place. But just as real files are accessible by file-aware commands, so are the virtual files. And in this particular case the file system semantics offered by the kernel included deletion of what shouldn't have been deleted.
HTH