Yeah, that's trivial to bypass on a compromised machine without touching their binaries or hijacking system APIs.

To be fair, most things are trivial to bypass on a compromised machine. In fact what would even be the point of loading arbitrary code into Notepad++ on an already compromised machine?

The author of Notepad++ even said it, "It doesn't prevent your original notepad++.exe from being replaced by modified notepad++.exe while the CIA is controlling your PC."

If CIA is already on your compromised machine and they want to target user of Notepad++, then they would just patched Notepad++ itself.