This demonstrates a fundamental lack of understanding of how computer security works. [snip a lot of superficial lecturing]
It's great the way you assume I don't know any of that basic stuff, because I come to a different conclusion to what you are sure must be correct. Anyway, couldn't be bothered explaining it to you.
As far as I'm concerned, my machines are an extension of my own mind.
And you think it's okay to let any random bit of software read or write anything in your mind... Okay. Good luck with that.
Bzzzt. Basic logic failure, symptomatic of your approach to many issues. Did I say it does or should work both ways? No, I didn't. Nor did I suggest allowing random software to write anywhere in the filesystem. You just assume there's only one possible protection model, and it's based on user permissions. You're wrong.
However, the question of what external information you allow to influence your understanding of whatever, can actually be a useful analogy for computing systems security. You should think about it.
Things like 'Windows (system) file protection' and all other per-user protections and customizations are something I have to go to extra trouble to disable as much as possible, on every Windows install I do.
Only because you can't imagine any other security method.
Can you name one other modern operating that doesn't go down this route of making things more secure? Android, OS X, iOS, Firefox OS, Linux and the various BSDs all do it. If it was such a terrible idea you would think that at least one major OS would offer an alternative.
Argument from majority view, aka appeal to authority, is invalid reasoning. 'They all do this, so it must be the right and only way'.
And it's working soooo well, isn't it? All these heavily secured systems are totally immune to all kinds of hostile code, right?
For instance, the NTFS 'protected system folders' are insufferable to me.
Indeed, why would anyone want to suffer from having their system folders protected.
Indeed, why would anyone want to even be able to see or touch _any_ of the system at all? Why not just make it all totally invisible and untouchable? Then we can all just assume it runs by magic, and all that magic is entirely benevolent and totally acting in our interests, doesn't spy or anything like that, and couldn't have been done better by any human.
(To answer that absurdity, I point in the direction of Windows 8, and the soon to be equally or even more loathed Windows 10.)
Darn it.. I wanted to link a really good article about file system abstraction and hiding in MS operating systems, but I can't find it just now.
I've probably read it. FS and registry abstraction was one of the biggest improvements in Vista. Microsoft finally stopped applications being able to shit all over the filesystem any time they wanted to. That alone killed a lot of malware and crapware in an instant.
Wow. So you know about that, and actually think it's a good idea. I'm stunned. Are you sure you are human?
Also ALL file systems are susceptible to corruption (spare me any claims to the contrary), and although this can be made less so, the overheads required are imo not worth the trouble. Especially since the #1 cause of file system corruption (in personal computers) is unexpected power down during writes, and this risk could be completely eliminated by simple hardware-software measures such as an adequate PowerFailWarn interrupt, slightly longer and guaranteed power supply hold-up times, and software that took care never to begin critical tasks it can't guarantee to complete within the known power-good window.
Again, every single modern filesystem uses journaling and other checks to prevent corruption. The overhead is minimal, and it protects against the scenario you describe.
Except when it doesn't. Please don't try and pretend it's impossible for journalled filesystems to get in a snit.
But do we see _that_ cheap & easy improvement in the PC architecture? Noooooo.
Perhaps because it is neither easy nor cheap.
Except it is easy and cheap. Sole reason it isn't done, is that MS-Intel have no actual interest in making PC systems more robust, or capable of controlling real world machinery that requires guaranteed reliability. (Btw If they had such an interest, there wouldn't be any such thing as the Registry.)
At least with FAT32 the structure is well known, relatively simple and can be hand patched in an emergency. Not so NTFS.
NTFS was released in 1993. It is 22 years old.
Remind me again how long it took the Linux guys to reverse engineer NTFS enough to produce reliable NTFS drivers that could actually write to an NTFS partition without randomly trashing it. Oh wait, never mind, I think it was about 2007. Wasn't it nice of MS to not publish the specs? (Did they ever?)