A tooltip like this would probably be adequate to resolve this problem:

You can manually tag pages as disambiguation pages. Manually tagging disambiguation pages is almost never needed, as the tag is added automatically by disambiguation templates.

This is consistent with other tooltips in the dialogue, which begin "You can...", and explains that it's almost never necessary to use it.

This is probably not difficult to do, but it's still not a priority. Might be a nice project for a student to do, or something.

Almost always, this tag is put into a disambiguation template, so even the most experienced of editors aren't aware that the tag exists because they never see it and never have to add it.

I can't even find it in Template:Disambiguation, TBH, however: I believe that policies point to using a template, not a magic word, for tagging a disambiguation page. So why would we encourage using the latter instead?

In T187116#3967928, @Elitre wrote:

I can't even find it in Template:Disambiguation, TBH,

It's in Template:Dmbox, which is the template that is used on Template:Disambiguation:

}}<!-- 
  Magic word for disambiguation pages:
-->{{#ifeq:{{{type|}}}|disambig|__DISAMBIG__|}}<!--

however: I believe that policies point to using a template, not a magic word, for tagging a disambiguation page. So why would we encourage using the latter instead?

It's not an either-or situation. The magic word doesn't do much for people, but it does a lot for machine readability. People add the template, and the template adds the magic word, so both humans and machines get what they want.

In T187116#3967947, @Deskana wrote:

In T187116#3967928, @Elitre wrote:

I can't even find it in Template:Disambiguation, TBH,

It's in Template:Dmbox, which is the template that is used on Template:Disambiguation:

}}<!-- 
  Magic word for disambiguation pages:
-->{{#ifeq:{{{type|}}}|disambig|__DISAMBIG__|}}<!--

Not everywhere, though? It's only on 50 Wikipedias or something. (maybe it has a different name elsewhere.)

however: I believe that policies point to using a template, not a magic word, for tagging a disambiguation page. So why would we encourage using the latter instead?

It's not an either-or situation. The magic word doesn't do much for people, but it does a lot for machine readability. People add the template, and the template adds the magic word, so both humans and machines get what they want.

I am not here to discuss the merit of the magic word itself :)
I am simply unconvinced by the need for featuring prominently something that isn't the only, or even the main, way to make a disambiguation page: it seems like a recipe to get some users unknowingly in trouble. Someone else will likely have to "clean up" after them for using code that isn't necessary, or could shout at them for not using the template as they "should have done", if you know what I mean :)

In T187116#3967986, @Elitre wrote:

I am simply unconvinced by the need for featuring prominently something that isn't the only, or even the main, way to make a disambiguation page: it seems like a recipe to get some users unknowingly in trouble. Someone else will likely have to "clean up" after them for using code that isn't necessary, or could shout at them for not using the template as they "should have done", if you know what I mean :)

I agree. In T155778#2955689 I found that dewiki once had three direct uses of __DISAMBIG__ in articles, and all of them were not correct.

@Schnark What one wiki does is rather irrelevant.. from a design point of view (taking into account 900 wikis with different templates) we need to find something better I guess, but I haven't heard too many suggestions on this front.

In T187116#4035235, @TheDJ wrote:

@Schnark What one wiki does is rather irrelevant.. from a design point of view (taking into account 900 wikis with different templates) we need to find something better I guess, but I haven't heard too many suggestions on this front.

Of course, one wiki doesn't signify, but I just went through https://www.wikidata.org/wiki/Q6148868 (only Wikipedia, and only languages starting with "a", after that I got bored), and all except https://av.wikipedia.org/wiki/%D0%A8%D0%B0%D0%B1%D0%BB%D0%BE%D0%BD:%D0%A6%D0%BE_%D0%BC%D0%B0%D0%B3%D0%86%D0%BD%D0%B0_%D0%B3%D1%83%D1%80%D0%B5%D0%B1 and https://azb.wikipedia.org/wiki/%D8%B4%D8%A7%D8%A8%D9%84%D9%88%D9%86:%D8%AF%D9%82%DB%8C%D9%82%D9%84%D8%B4%D8%AF%DB%8C%D8%B1%D9%85%D9%87 have the __DISAMBIG__ included into the template.
So I think it is justified to say that a large majority of wikis would prefer the users not to fiddle manually with that magic word, and the checkbox in the settings dialog is useful only for very few wikis.

Well being in use, is something already covered by T155778, Adding is more complicated I think.. Annotations in TemplateData ? or some sort of automatically generated list (by the transclusion in the parser) exposed as an api ? then you can query that api and show it as an autocomplete list in the dialog.

I don't think this is a good task for the good first task tag, I'm not sure myself how it should be explained.