Yeah, I had mentioned that it was weird that Brandon made up two of the metals, when everything else existed IRL.
As far as spawning in one place, I believe this is only mentioned in a conversation between Kelsier and Ham, so it is possible that it spawns other locations. According to Wiki, Chromium in it's native form is rare, with a mine in Russia being the only one listed. I know there are other metals concentrated in certain geographic areas, so Atium forming naturally in one area is not unheard of.
Contracts. There is obviously something more to this story, however it could be something as simple as trying to keep as much out of TLR's hands as possible or because it is easier to hold one Atium nugget than a huge purse full of coins. If they really needed the atium, I don't see why they wouldn't just find a way to sneak into the Pits of Hathsin and get it themselves. They could eat some guard and prisoner bodies or something and being natively blind might locate it much easier than Skaa could.