"Luckily Linux seems not to honour that crappery on files but removing Microsoft malware from the registry can be a problem."
There are some things even root can't remove. Like things under control of the kernel like a zombie process (something locked in something like an I/O wait state that'll never clear). That was the thing with that North Korean OS mentioned a while back. A lot of the Big Brother stuff is baked straight into the kernel, to the point that not even root can mess with it.