Using nightly vlc-3.0.0-20170910-0457-git-win64-debug I was able to extract the MPEG AAC Audio (mp4a) audio stream from a .webm video file. The resulting .m4a file plays fine in VLC 3 and VLC 2.2, hooray.
However Google Play Music's Music Manager app refuses to upload the .m4a audio file, with "Unsupported format." When I look at Codec information for this file, it has a new piece of information, "Bits per sample: 32", that isn't in the Codec information for other .m4a files I successfully uploaded to Google Play Music nor is it in the original .webm file. Google Play Music supported file types says "ALAC (.m4a) 16-bit files supported", so I think VLC's switch to 32 bits per sample makes Music Manager unhappy. Is there any way to set VLC's mp4a encoding to 16 bits per sample? There's nothing I can see in the convert profile options or in VLC Tools > Preferences.
A workaround is to convert the audio to an MP3 file in VLC.