Exactly!
It is quite a good and pargonal example of where the power of DT contradicts its UI/UX, IMO.
That is because the different functional domains are never really explicated to the full.
So, the sad thing about is: it is great! Then, the way things work most people who would benefit from it will probably either never find out, nor come around habituating it. That is everyone that is not approaching DT with a technical/tinkerer/nerd mindset.
IMO it only starts w/ the ambivalence of the terms, i.e. “annotation” being used in different contexts and (technical) meanings in the same UI.
So, finding a distinctive and evocative term (like “aside”, “note attachment” or anything…) would already really improve and “unclutter” things dramatically for the ordinary user.
Another example where things just are way to byzanthine in terms of UI/UX is the very fact you mention, and one which I would read as an index of some deeper confusion/obstrusiveness w/ regards to UI/UX:
it takes a lot of time and effort to process the very fact that something that starts as a box in the rather technical/finegrain realms of somewhere in the right sidebar then becomes a full grown document-of-sorts within the DT-document-ecosystem, attaining all those powers that autonomous documents have in DT.
It is just not very intuitive and transparent.
And I am not only talking about discovering it.
But as everyone with non-technical mindset – and within UX – knows, this is also true for dedicated users which just constantly have to work ‘against the system (UI)’, and/or who have to remember that there is a script sitting somewhere, or there is just another shortcut to that which I have to remember.
The UI would already do much better in this regard, if it would allow creating that annotation document directly from a context/right click, directly linked to pointing to (clicking) any particular document.
After all, it jsut doesn´t make sense from the logics of real-world use that right-clicking a document you can a) OCR it, b) set a reminder (after all DT is not a task manager), and c) stamp it … but not annotate it directly.
I see that very often even in venerable apps. They are adding modules and features – but rarely they think in UX and workflows. It´s a shame because most users are just that: users, not engineers-by-mindset.
So, “annotations(2)” rock! In theory. As they are not really put on stage in proper dress and with proper accompaniment tunes…

PS: yeah that script really is one of those ‘easy ones straight from heaven’. But then, it steps in for something that shouldn´t sit in the scribes cellar/department, but really be on center stage… 