Earlier quoted context omitted.
Do you have a proposal for a system that properly integrates alpha and layering without the notion of a stacking context?
If by "stacking context" you mean "one global context," then no. But if you mean stacking contextS as described by the article, then Win32, Cocoa, Swing, Qt, wxWidgets, and probably Gtk are all examples of a system where z-index doesn't involve reading an article. I've come to the conclusion that HTML is great for content that looks like 1999. But in 2016, every time I use HTML and CSS I end up dealing with some subs…
Not to mention that the layout model itself is painfully limited. The other day I tried to implement a card layout --- that is, a box containing a bunch of components all arranged in the same place, with the box itself being the maximum size of the components inside. As far as I can tell this is simply impossible in HTML without explicitly sizing your layout, which rather defeats the point.
I'm currently working on a web app based on Polymer. This helps a lot, as it gives me a nice modular framework with composeable components and local namespaces, which takes a lot of the edge off some of the pain of CSS. But that just casts the pain of trying to design UIs in HTML into stark relief.
...I did once find a pure Javascript layout engine; it didn't use HTML layouts at all, and positioned everything using code (and CSS transforms). They claimed to be actually faster than stock HTML.