The reason it doesn't work as expected is because the mechanism used to start the remote stream reads the play alias first to get the stream name that it then passes into the stream alias part. If you remap the name in aliasmap.play.txt, it will try to start the wrong stream name.
The easiest way would be to use a different name for playback and alias that to the name used to start the stream originally.
original stream name is myStream. This is the remote stream (ip camera for example)
transcoded stream name is myStream_360p. this has the overlay.
playback stream name is stream1. this will be mapped to myStream_360p
The first line will map the player request for stream1 to myStream_360p.
the second line will pass thru any other stream name unchanged. This will include any direct requests for myStream_360p or the request to start the remote source.
Because you cannot use .stream files to start your remote source, you need the following in your aliasmap.stream.txt file.
To start the remote stream, use Startup Streams and use myStream and the mediacaster name. You can also use the old stream manager on http://[wowza-ip]:8086/streammanager to start it manually. Either way will have the stream show up in the list of published streams for the application.