In this case we can't even use the image itself as a mask, like for some spells. It becomes too transparent.
Yes you could...
Formats war... Just like apng was developed and mostly supported by mozilla
Actually apng is a really decent sh!t... PyTom think so too and he looked into it, Ren'Py can support it, it just requires time and effort to implement and he said that he'd do it only if it trully went mainstream. There is little point in it right now becausem even less people know how to encode apng than .webm

Yeah unless they fix it best would be masks.. but that needs 1 files right ?
Look at our animation and their sources. Quality of Ren'Py webm implementation is just as good as .png sequence. At times, it is not even possible to do a .png sequence that can be rendered at the same speed as .webm by Ren'Py (but we do not have frame-rates that are anywhere near that). Size so far has always been smaller (sometimes likes up to 8x smaller than .png and 50% - 400% smaller than .gif).
I've explained it really well above, you need one, plain and simple .webm and another .webm where alpha channel is encoded to red channel.