I'd like to get for track 1 "Audio #1" and for track 2 "Audio #2"

"Audio #%StreamKindPos%" but it does not work well in case of only 1 stream

Also it would be very nice for me to see the used Encoded_Application, Encoded_Library and the Encoded_Library_Settings. If available. Is there a way to show these in another section then Video?

They are linked to video, why putting them somwehere else? Encoded_Library and Encoded_Library_Settings are also in the General part in case data is about the complete file.

Is there a way to view the ScanType in a "short" way?

currently not possible with current template engine, you need to use something else after MediaInfo for changing that.