Does the Transcoder Add-On support audio resampling; and if so, where in the template would this be set?
No, you cannot change the audio sampling rate using the Transcoder. It will use the same sampling rate as the source.
So, Flash Player’s microphone capture with Speex works at 16KHz. And I can confirm that the Wowza Transcoder keeps this sampling rate for AAC, which is problematic when mixing other live streams that are more standard sampling rates of 44.1KHz. Is there still no way to force a sampling rate change for AAC encoder with the Wowza Transcoder? Otherwise, is my only option to downsample all other content to 16KHz?
There currently still isn’t a way to change the sample rate in the Transcoder.