So the thing to remember is that Drawabox is not focused on texture and detail - while we do touch upon it, the course is primarily focused on construction, and it becomes very easy to get distracted from that core focus. In general, don't look at Drawabox as being a course to be combined with your particular goals - I understand that there are particular things that you will want to focus on, but the course is designed in a particular way in order to develop very specific skills and understanding. At this stage you aren't equipped to modify that approach properly.

In regards to the wings, you actually did cut back into that wing several times while redefining the silhouette. Your intended strategy wasn't wrong, but the execution was off, and the use of your brush pen to do it compounded those mistakes. You should only be using your brush pen to fill the cast shadow shapes (even the outlines of those shapes should first be drawn with your regular fineliner). You can see a better way of handling the feathers as shown here, but before that the wings themselves were drawn to be quite flat, and this also impacted your result.

The drawings we're doing here are at their core about learning how to communicate visually. Through construction we communicate to the viewer what it'd be like to pick up the object and manipulate it in their hands. It gives them the spatial understanding of the structure, how the forms fit together and so on. Through texture, we communicate what it would be like to run our hands over that surface, to understand the nature of the little textural elements, and how they're spread out over the surface.

The thing to keep in mind is that everything serves a purpose here, we are transferring a bit of information that we feel the viewer requires to fully grasp the totality of the object. When we get into the territory of "making a pretty picture" is when we instead start thinking of it more as decoration, taking steps to add detail for detail's own sake. This is definitely still a confusing concept, but one key issue is when students jump to detail before fully fleshing out the construction. A solid construction with no texture still communicates 90% of the information the viewer will need, with the texture itself constituting just the last 10%. Many students who are focusing more on just decoration will end up communicating only a small portion of the construction, plus 10% from the detail. This results in far less than even the 90% we'd get from the construction alone.

I can see now that you made certain decisions because you were eager to work with your brush pen - but in doing so you broke away from the actual instructions you were given, which was to work with a specific kind of pen.

As to the organic intersections' shadow outline, that would generally be okay, but in this case it didn't come through clearly because that particular shadow was not consistent with the other shadows in the scene. The shadows you had filled in suggested that the shadows were coming a little more forward, as shown here.

I hope that clarifies any confusion.