For example most 18650 use the case as negative and the positive as an isolated pin, but some flat batteries are reversed - the metal case is positive and a isolated pin as negative. Why is that?
All Li-ion prismatic cells (not LiPo, those seems to use two separate pins and the metallic envelope is isolated) that I saw are so. The small pin at center is negative and the whole case is positive :S
I'd have to say it was design restrictions in devices initially. You see this in watches, mini alarm clocks, and other miniature electronics where the cover is either plastic or not designed to be a conductor, just a dust/dirt/moisture protector.