If you go to https://www.stackoverflow.com then you will notice, that the header is fixed and always visible.
Why is this not the case at superuser?
stackoverflow and meta.stackoverflow sometimes have different UI code than the other SE sites. IIRC they run on a separate server too.
The header of this site is not fixed, because _________ (fill in the blank). They're probably in the middle of a UI update and only wanted to test it on stackoverflow.com until it's ready to go for the other sites, but that's just my guess.
Stack Overflow is essentially running "updated" Stack Exchange software.
There are many features in use on Stack Overflow that are not relevant to other sites.
The platform is also still under active development and feedback. They may well port UI changes over to other sites as the platform matures, but as they say "if it isn't broken, don't fix it".
We work well at the moment and it only makes sense to update the other sites when there is a clear benefit to do so and it outweighs the potential problems an upgrade might cause.