Hm. I think it can be achieved by manually adjusting brightness and contrast for the alpha mask. But it's a tedious work.
I am not sure that it can be achieved even then

When the images were merged with black background, original transparency information was lost. There may not be any (perfect) way of recovering it working with an image as a whole. Best two (quick) ways right now are this:
1) GreyScale all frames and use as a mask. You get a version where the transparency is way below the original.
2) Remove black matte. You instantly get (about) the same thing. After converting colors to black (all rbg color values to 0) and use that as a mask for webm, you get a very sharp image but with some information lost (you don't see the handle of the ice sword for example). Otherwise there are no artifacts of any kind.
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The very best way to recover the lost information (imo) would be to remove the matte and write a script that would go over every frame pixel by pixel and increase pixels alpha based of predetermined range (low increase for high alpha, 0 increase for 0 and high increase for low alphas) but it's not something I want to write atm

Edit: Maybe some color information is lost as well... it'll prolly require a genius to get it right...