I actually think it's quite important to clip against brush models, and I wouldn't have put this tutorial out if I hadn't got that part working.
OK, so ammo boxes and the like can be ignored, but doors at least need to be included. The way I see it is that not clipping against doors could let you see some of what's behind a door, and besides - it looks unnatural.
Also, the thing with the view going inside the player - that's not a bug, it's a feature.
Joking aside, if we're clipping against walls then the view has to go somewhere if you back up against a wall. The choices are inside the wall, inside the player or somewhere inbetween.
Somewhere inbetween is right out; the player model is not defined by the actual verts and tris in the model, it's defined by a bounding box, which would virtually be in contact with the wall in such a situation. There is no inbetween.
Inside the wall is out because you would need to know the dimensions of the wall and how it related to everthing else in the world otherwise you risk visual artefacts (and it's the whole point of this code to remove these, so that would defeat the purpose).
So inside the player it is. Turning the player model transparent when this happens is a compromise, because in cases where the view is so close behind the player (and this applies to even using the view inside the wall) the player model will actually occlude most of the view. This way you still get to see somthing.
Another option might be to do what Tomb Raider does and swing the view around to in front of the player. To my mind that kind of thing goes well beyond the scope of what is supposed to be a first-person shooter. It's an exercise for you to do yourself if you want it.
So yes, it was a deliberate choice, and yes, I was completely aware of what the options were and what was good and bad about each of them when I wrote that code.