ffmpeg v4.0.2 or higher can encode/transcode VP9 in mp4.
Commandline (when transcoding): ffmpeg -i INPUT.MKV -c:v vp9 OUTPUT.MP4
Commandline (when remuxing (Super fast)): ffmpeg -i INPUT.MKV -c:v copy OUTPUT.MP4
ffmpeg v4.0.2 or higher can encode/transcode VP9 in mp4.
Commandline (when transcoding): ffmpeg -i INPUT.MKV -c:v vp9 OUTPUT.MP4
Commandline (when remuxing (Super fast)): ffmpeg -i INPUT.MKV -c:v copy OUTPUT.MP4