While im not Uncomfy, I may have an answer that can help.

About drawing through things:

See, we draw "through things" because it helps us to develop our understanding of 3D forms, and how those forms sit in space.

For example, when drawing boxes, drawing "through them" as if you had x-ray vision, gives us a good understanding as how that box sits in 3d space, its hard to say, but it gives you a really good sense of how your forms is constructed, drawing through a box also happens to be very useful at understanding our mistakes with the convergences of a box.

While not related to Drawabox, drawing through things can also help to solve draftsmanship problems, like for example, say you are drawing a head inside of a box, it is really convenient and useful drawing through that box in order to fit for example the ears, or another example would be when drawing hands, when you want to draw a hand you need to know where each finger is located, and so, you need to draw through your forms in order to get a good idea at where are your forms placed in 3d space, if you were to just simply draw your hand without drawing through it, you could potentially get wacky or wrong placed fingers.

About the contour exercise:

Note: I will be refering to Lesson 2 "Organic Forms with Contour Lines exercise" as i think is a simple and good way to get the point.

Now, when it comes to the contour lines exercise,it may be kind of weird that we only need to draw the portion that is visible, but i personally like to think of it as 2 exercises aimed to teach you different things.

The first one, where the draw the entirety of our ellipses is meant to show you how the degree shift of the ellipses changes relative to the position of the viewer, and in doing so, it prepares you to think more about how your forms and ellipses change as you or the object moves in 3d space, it also teaches you numerous things like, fitting your ellipses within the sausage form, fitting your ellipses with the minor axis, developing your muscle memory to draw entire entire ellipses, etc.

However, there's a problem, drawing through ellipses in my opinion its not really that helpful when we want to convey how exactly is our object facing us, and so, the second exercise comes in handy, see, contour lines are incredible powerful at conveying how the object is facing us, because we can tell 2 entire different stories depending on how we place our contour lines, if you draw the visible portion of the ellipse, you could be telling the viewer that the sausage is looking at a specific direction, if you however, draw this portion of the ellipse the other way around you could the telling that the sausage is looking at a completely new direction, and it doesn't stop just with the direction of the sausage, depending of the "visible portion" that we are seeing from the ellipse, we could be telling that the object is facing us or not.

This is a good example of it notice of we are telling to the viewer that the sausage is changing directions depending of the portion that we draw of the ellipse, this is something that you couldn't do if you draw fully through your ellipse, unless you use line weight.

Also, in my opinion, overshooting your ellipses like the exercise ask you to do, makes you think a lot more about the turning of your forms and it will come at handy later on.

And ultimately, it is also more flexible to just draw a portion of your ellipse, later on when you tackle more difficult things you wouldn't want your construction to get messy by just drawing full ellipses, but i guess it depends on what you are doing.

(PD: also a reminder that what we are doing is just an exercise, outside of drawabox, you can draw in any way you like)