system
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Process hacker has kernel level access, from which it can do anything to any process/file/hook/etc, likely including dll injection into application level.
The point is to prevent unknown 3rd party programs from gaining kernel level access, not to try to defend against them after the fact. Sure, you can add certain mechanisms to counter specific kernel program functions, but they can be easily bypassed and can add performance overhead and software incompatibilities.
No protection feature can protect you from a rootkited host.