I wanna say yes and and improve the Index Post-It idea. It makes navigating in the digital notebook almost impossible when you don‘t have guiding index post-it‘s on the side, especially if the content of the study is already quite big by it‘s nature, like the German Grammer. Having the ability to put it would make Goodnotes equal with the paper book alternative. But having it as a Structure-Tree would make it even better.

I have drawn a simple UX Sketch here. The idea is to give the Content Structure Tree its own extended module to be able to freely modify and navigate in it. The more subpages/tabs a Header have, the more toned it looks in the UI. It is easy to change the order of subpages and tabs by press hold+drag and put colored index post-it, sticking out at the wrapped up view anyway. In the wrapped up view, we only see the Headers and that gives us a quick orientation, before we dive in to the content. Being able to see the content in Headers and bounded Subtabs enables us to zoom in and zoom out from the content, or dive in to a particular sub-subject, so we don‘t get mentally lost in it.
I have added the Screenshots of the Solidworks Feature Manager tree in the images. Also a visual Tree. Such files with complicated Feature Trees can be a good inspiration at the development of the UX Module.

Since this Structure-Tree idea is essentially not not an invention and already is the base of many programms, I am assuming that it would be also quite feasible on the back-end.

ps. There are studies showing that one of the major disadvantage of learning from a digital tool that prevents the efficiency of learning, is that loosing the relational ties in between the pieces of information blocks. Because with the tactile thickess of a book, we subconsciously measure the distance in between the content blocks from one another and form a structure in our heads. Such Structure-Tree can be a good solution for our cognitive learning processes since there is no thickness value of an iPad document and can actually be an interesting research subject if it would existed (thus we need the bulky looking UI when a Header is overwhelmed with Subpages -not only to seize the relational order but also to feel how big/small room they occupy spatially. Example: Correct Writing would weigh 1/100 lighter compared to Verbs in German Grammer but they both would be same looking Headers if no visual UI signal is given).