Ah, I might have missed the point of your question.
Maybe you’re wondering why Ubuntu suggests updating the package although you were already using 4.0.1.
It seems that the “PPA for KiCad 4.0” is often rebuilt (daily?), see:
There probably hasn’t been any meaningful change since the day 4.0.1 was released but Ubuntu doesn’t know that, because the changelog contains the build date. Here is a list of the latest changes to the binary package:
https://launchpadlibrarian.net/236923526/kicad-doc_4.0.1-0.201602041347+866~12~ubuntu14.04.1_4.0.1-0.201602080146+866~12~ubuntu14.04.1.diff.gz
I will tell the maintainer, hopefully we can fix this.