@pius-lee is right. Adding -vf "premultiply=inplace=1" to the -auto-alt-ref 0, fixes the alpha in vp8.

This command went through and kept the alpha info intact

ffmpeg -i input.mov -c:v libvpx -b:v 2M -pix_fmt yuva420p -auto-alt-ref 0 -vf "premultiply=inplace=1" output.webm