You can match template names with stream names, and remove the specific template name (i.e.transrate.xml, transcode.xml) from Application.xml file.
if you only have a template named myStream.xml you will only transcode streams named myStream. if you also have a template named yourStream.xml, streams named "myStream" and "yourStream" will be transcoded using those templates, and other streams will not be transcoded.
You could take a look at the ILiveStreamTranscoderNotify and ILiveStreamTranscoderActionNotify interfaces. and dynamically choose your template file. Setup the following event handlers as indicated in this
post. Then you can choose the template required by leveraging the liveStreamTranscoder object within the ILiveStreamTranscoderActionNotify.onInitBeforeLoadTemplate event handler as follows: