How can I force YouTube to convert my video's audio stream to Opus or Vorbis / Youtube Red issue
YouTube currently does not have any encoding options for content creators. 

As far as why some videos are encoded as webm and others in different container types, I don't believe there is any documentation on that whatsoever. YouTube may be beta-testing specific codecs, to see how codecs perform/stream for end users, or there may be a specific matching system whereas input = specific output attributes. 

When you upload a video to YouTube, the video is re-encoded using a Variable Bitrate at the highest resolution / matching resolution of the original upload. If the uploaded video is larger => 360p then smaller versions are also encoded for multiple streaming options (240p as an example). 

But there is no current way to force the YouTube encoding platform to encode to a specific codec, and even you were able to figure out what input codec would result in a specific desired output codec, it may only be temporary. I only mention this because YouTube has stated it is currently experimenting with new codecs, including closed source proprietary codecs and encoding algorithms... so what works today may not tomorrow.