Actually, Windows could merely encrypt the atom tables and use checksums to verify them. It would be impossible to inject anything into them. Those articles, while containing an element of truth, obscure more than they reveal.
And Skybird is right. System file check does nothing to prevent alteration from happening. It detects and corrects, much like antivirus or antimalware software does. We're generally happy with how the latter two categories of software work, why would we not be similarly protected by periodically doing an "sfc /scannow" to eliminate alteration of system files?
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