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If you select the individual sound file in the movie's Library, and then right-click and select Properties, you can set the compression for each of the sound files individually. There is no override setting for the audio output for the html5 Publish settings that I can see.
Yes, I already pointed out in the first post that you can change the compression at the individual asset level and that there doesn't seem to be any way to change it in the publish dialog.
Seems a bit absurd that the ability to change the default compression got left out of HTML5 mode. This has been core Flash functionality since pretty much forever.
Well, I at least discovered what was causing the loud CLICK at the end of the generated MP3s. Turns out the Flash CC importer for WAV files is a bit dim at telling the difference between audio data and metadata. Re-saving my WAV files without metadata fixed the clicking issue.