Hey thanks for the reply. When I noticed the scratching my pencil had the space-gray coloring that came off the iPad like on the last picture I attached here. I was able to wipe that off quite easily but the black dot remained. I tried to get it off the pencil with my finger nails but it was still not coming off. I am pretty sure it's not external but protruding from inside like you mentioned. I have seen many threads with this problem and they all had this black dot on their apple pencil in common. One even had a really detailed photograph, shot with a DSL camera, in which you could very clearly see the metal sticking out (attached).
As for traveling. Nope. I bought this iPad for university and I mostly used it at home. Because of the pandemic almost all of my classes were online. I did bring it with me to the library and to class a few times. Also I noticed the dot on the day I noticed the scratching and after that I only attached my pencil for charging.
You're right though. It might have moved in my backpack, but in the end it all comes down to that metal dot causing this. Plus isn't the iPad expected to be carried around with you?
Now that I know about this scratching problem, in retrospect of course I wish that I had used a silicone case for the pencil or a case like it was posted here where the magnetic side of the iPad is covered too. But I used a case were the side is free (like the original apple cases) so I can leave my pencil attached all the time. Isn't that the upgrade to the old airs, anyways? If I get my iPad replaced (even in my dreams) I will take these precautions but still in my opinion all of this shouldn't happen with normal use.