Hi,
Version number is not taken into account. Otherwise, all the files would always be listed, which would render that list of file useless.
However, please note that the list includes all the patches from the first build of the 4.4.1 up to the last.
So if you updated to the 4.4.1 several weeks after it had been released, some of the patchs that were listed under the 4.4.2 were already in your 4.4.1 build. And thus, when you compare the changes between your 4.4.1 build and the 4.4.2, you might see no change because the patch was already there.
Also, for the email files you're talking about, these were modified between the 4.4.1 and the 4.4.2, it's a bit of a special case. These files were modified at some point between the 4.4.1 and the 4.4.2, but the changes were reverted in order to move the changes to the template files. But for the script we're using to generate the list of files, these files still appeared due to that temporary modification.
However, regarding the media/css/frontend_default.css file I'm not sure what you mean. That was was changed a lot.
Here is a screenshot of the commits on that file:
i.imgur.com/WT5U6En.png
And here is a diff of the changes in that file:
dl.free.fr/mffKpmwQq