I expected you to like "tricky" things :-). The problem with z-indexing is that the index varies a lot, depending on e.g. a Category entry.
We used z-indexing when working with BasicInternet:Home to add the social media. And I really like the Category entry, provides me a hint for further look-up.
But the most important one for me would be that the namespace footer "copies" the settings of header/footer from the skin. (not like in IoTSec.no, where the I have white on grey for the namespace footer, and black on white for the page footer)
the formatting comes from the id=cwi-footer or bif-footer. But I have not found out how to a) change the color of the "links" (it's not color:) in MediaWiki:Hf-nsfooter-IoTSec. Only background works, changing to grey.
What I'd like to see: same colour combination as the "skin footer".
Okay, it appears that the per namespace footer extension ignores CSS defined in Common.css.
However, all is not lost as the CSS can be defined in the skin definition main.css. So I have defined black links. I also removed the hardcoding of the background and also sorted out the vertical alignment. I'll also define a h2 rather than hardcoding 120% font size for the headers.
Regarding the overall footer question. I am beginning to think that where we have a custom footer, we simply switch off the MW footer and simply add the Upload File / Special Pages etc links into the custom footer.
I've had a go at this on the IoTSec skin (even tried it logged out!). Let me know what you think. Do non-logged in users need to see the Discussion, History etc toolbar? If not, we could hide it from non-logged in users which will make the footer look completely merged for those people.