Merge two transparent webm videos with FFmpeg
Since 2016-07-20, it's possible to decode properly a webm with alpha channel (VP8a or VP9a) but you need the -vcodec libvpx option. You must download an FFmpeg compiled after that date (or compile yourself with up-to-date commits) and use the following command:

ffmpeg -i logo.webm -vcodec libvpx -i cortina.webm -filter_complex overlay -vcodec libvpx output.webm


Note that -vcodec libvpx is before the input that needs to be read using the alpha planes (in this case, is cortina.webm the overlaid video, thus we put the option just before it).

(As Mulvya states, the format conversion should be avoided in this case.)