When a stream is published to Wowza, it also becomes available for playback at Wowza output. In addition to this stream, if you also have the Transcoder addon enabled, the transcoded stream will also become available at Wowza output after it has been transformed by the Transcoder.
The warnings you are talking about are referring to the un-transcoded stream. Since your source is using Speex audio codec, the warning message is informing you that this particular stream is not supported by iOS devices since they do not support this audio codec.
You should't get messages related to the transcoded stream.
Are you using the template named audioonly.xml in the Wowza /transcoder/templates folder. Use that template as a starting place. The name is a little misleading, it just means that it only transcodes the audio, not the video. The video is set to PassThru. That is the Transcoder template that is used in that article. Start with that, test it as-is before making changes.