"Is it possible to get Wowza to use a different Format profile and Codec ID for the container so the file directly will be playable on a android device?"
No, I think you can only chose an .mp4 or .flv container. You can start your stream from the stream manager with flv:my.stream Just a guess there.
For whatever reason your android device prefers the "Kodak Base Media isom" container. You have several options. You can re-encode as you were, perhaps in conjunction with a Wowza module. You can play the files as a VOD stream on your Android, in an Andorid player using RTSP, or in your Android browser using RTMP and a flash client like the Wowza SimpleVideoStreaming example. If you're copying the file over you can try using a different player.