Like the title says, I am trying to find out if VideoIO can handle dealing with pixel data that uses the alpha channel.
It does not, the list of supported pixel formats for video writing is here. I don’t think many codecs support an alpha channel, maybe VP9? I would try to get a pipeline going with the ffmpeg cli and then write to that on stdin. FFMPEG_jll makes it simple to find and install a copy of FFMPEG for your program to use.
An interesting post about Alpha with FFMPEG: