These containers are around 4" tall. I have a set of 3 metal dough containers with a lid. I think the total height is a bit under 8 inches. So, I see the issue, assuming your space is less than 12 inches.
Here is another idea: Pick up a roll of Reynolds non stick aluminum foil.http://www.amazon.com/Reynolds-Wrap-Release-Non-stick-Aluminum/dp/B005EF1YRY/ref=sr_1_1?ie=UTF8&qid=1357159500&sr=8-1&keywords=reynolds+no+stick+foil
It is 35 square feet and 12 inches wide. Assuming your containers are 6 inches or less, then you can cover the bottoms of 70 containers for about 10 bucks - 15 cents each. I have done this a few times when I knew I had a sticky dough and I was worried about the dough sticking to the metal containers. Just cut out a circle for the bottom and you are done. When you flip the container over, the dough obviously drops out. Then, the foil peels off - no muss, fuss, hassle, etc.
It is a bit more effort to cut out the circle but not a big deal. Better than staring at the dough hook going round and round while the dough mixes.
As an alternative: sometimes, if I have a stubborn dough, I just dust my hand with flour and the top of the dough. If I work around the edges, nudging the dough off the bottom a little bit all around, it then drops out fine.
Not sure what the cause of the black is on the pan, but has happened to me too. I think it is about new aluminum pans that need a thorough cleaning to get off whatever residual stuff is on it when it was new.