ffmpeg never puts cue points inside the webm's initialization segment, thus these are mandatory for Media Source Extensions API to play the video properly.
There are some tools which can fix the webm files right after the encoding process, such as mse_webm_remuxer and sample_muxer.
We should write our own muxer into Javascript so we don't have to ask the user to fix their webm file themselves, then add the cue points automatically inside the initialization segment section of the metadata file.