Because both transcoding engine does not work the same.
Kodi does not support transcoding, so as you enabled it Bubble is used. Seems Bubble keeps all the tracks inside the transcoded media so you have access to them.
Plex support transcoding and remove unwanted tracks when transcoding to the other tracks are removed so not here so you can’t select them.
Yatse should offer a dialog to select them before playback.
In all cases to stream to VLC you DO NOT NEED TRANSCODE so as I just explained to you enabled the audio codecs in the settings to avoid transcoding (eac3,aac, dts)