I was absolutely perplexed by something that seemed so simple at first. Later on, I acquired some mental trauma from tracking down a particularly nasty bug around alpha and PNGs. You'd probably not be surprised that once one becomes more or less familiar with the nuances around alpha channel handling, that nuanced bugs can crop up in even the most robust software. So... yes. 🤣
This is where I encourage folks to gain enough confidence in their own, hopefully well researched, understanding. Eventually, it enables folks to identify where the specific problem is emerging.
The skull demonstration has zero alpha regions within the "flame" portions. Following the One True Alpha formula, the operation should be adding the emission component to the unoccluded plate code values. There is no "scaling by proportion of occlusion" to the plate that is "under", as indicated by the alpha being zero. The author has some expanded commentary over on the issue tracker.
The following diagram loosely shows how the incoming energy, the sum of the green and pink arrows, yields a direct "additive" component in the green arrow, and the remaining energy indicated by the pink arrow, scaled by whatever is "removed" in that additive component, is then passed down the stack.
If this seems peculiar, the next time you are looking out of a window, look at the reflections "on" the window. They are not occluding in any way! Similar things occur with many, many other phenomena of course. For example, in the case of burning material from a candle, the particulate is effectively close to zero occlusion so as to be zero. Not quite identical to the reflection or gloss examples, but suitable enough for a reasonable demonstration.
Sadly, Adobe is a complete and utter failure on the subject of alpha for many, many years. If you crawl over the OpenImageIO mailing list and repository, you will find all sorts of references as to how Adobe is mishandling alpha. Adobe's alpha handling is likely a byproduct of tech debt at this point, culminating with a who's who of image folks over in the infamous Adobe Thread. Zap makes a reference to the debacle in yet-another-thread-about-Adobe-and-Alpha here.
Gritz, in the prior post, makes reference to this problem:
You can probably read between the lines of Alan's video at this point.
So this is two problems, one of which I've been specifically chasing for three decades, and one that relates to alpha.
As for the alpha problem, I cannot speak directly to AfterEffects as I am unfamiliar with it, but the folks I have spoken with said the last time they attempted, Adobe still does not properly handle alpha. I'd suggest testing it in some other software for compositing just to verify the veracity of the claims folks like myself make, such as Nuke non-commercial, Fusion, or even Blender. All three of those should work as expected. My trust that Adobe will doing anything "correct" at this point, is close to zero.
As for "colour management"... that is another rabbit hole well worth investigating, although it's probably easier to find a leprechaun than pin down what "colour management" in relation to picture authorship means to some people or organizations. Keeping a well researched and reasoned skepticism in mind in all of these pursuits is key. 🤣