You didn't read their paper properly. They make exactly the point that you are making. i.e. that "writing to disk", in most cases, does not mean physically writing individual bytes to the disk. The abstractions provided by both the language and the operating system help to make the obvious implementation as fast or faster than naive programmer created optimisations. In other words, this is a confirmation of the saying
premature optimisations the root of all evil
There is a WTF in the paper and it is their claim that Python doesn't run in a VM.