Ah yes the tragic story.
They do have the awful black Anti Aliasing with is Solved by the "add" blending tool .. however, i personally don't like that effect i think it washes them out. I -CAN- output the files to have PNG alpha channels and transparencies... but when i do, My photoshop script can't seem to arrange them right and... well I'm just not fanatical enough to arrange thousands upon thousands of frames 1 by 1 row by row on my own, checking all the alignments and such. If you know anyone who can script a photoshop script that could handle it, p0lease let me know. I'm still waiting