The point is, malware can't get into that directory without user consent. Having physical access to the machine, rebooting into safe mode and running commands is a stonking big user consent.
I can pwn my own desktop, yes, all I have to do is say "run as administrator". But the point of the security boundary is to make it impossible for software to get these privileges without me actively giving it to them.
If you're shifting the goalposts and imagining the computer does not belong to me, but to an organisation that I'm a mere employee of, they'll be using AD Group Policy to control what I can and can't do, and Bitlocker to encrypt the boot drive. I cannot boot into safe mode without having the tech support department give me a special code to unlock the computer. Again, that's how you get on the other side of the airtight hatch.