Another question to consider: what problem are you ultimately trying to solve? Under what circumstances will the proposed link be clicked? When the link is clicked, what information do you want to present to the reader?
The information I want to access / see is information that is related / has a context to the source information (the link is contained). E.g. one has a subject 1 in an item / folder / doc A at the beginning (of a story, a proof of a theorem related to another proof of a theorem or what ever) and at the end of the story one has a subject 2 in an Binder item Z containg text relating to subject 1 you want to see / access in this context. May be the same (of countless) reasons why one uses bookmarks / links within a Word doc / in other writing programs.
May be a good alternative (partially at least) would be if one could build Scrivenings which included marked text / partial areas (of Binder items) only of special folders / docs. So you have 50 Binder items contained in a Scrivening, 10 of them contain / show only special areas / text / pieces (one has marked before for instance).
I don't know what the answer is for your particular project. In my own work, though, internal links most often point to a definition, an image, or a reference, all of which seem to naturally have the kind of coherence that justifies creating a sub-document.
Yes, that is a proper way of using such links I would say. I do it the same way. By the way, creating links (or even Scrivenings) to other items / pieces of text to other projects would be very great as well.
If, instead, you're doing something like line-by-line commentary on a text, perhaps the solution is to rethink the layout so that the text and commentary are in such close proximity that links are not required?
Sorry, I do not understand, do you have an example? But to adapt the structure / layout to the need / position of links or so actually would not be a good idea for me, I suppose. And I would assume it is not possible (in a practical way). If one has e.g. 5 links in the same source information to different items / positions / pieces of text, etc. in the project, how could one do it?