Currently you can set a custom user-agent for the main Cordova webview by overriding the init method for the DroidGap class. However, when opening a page in the InAppBrowser, that webview will still contain the default user-agent.
There are two solutions that I have thought of to this:
1. Set the user-agent of the InAppBrowser webview to whatever the user-agent in the Cordova webview is set to. (This is what I am currently doing, as it was a one line change, but it requires rebuilding Cordova manually)
2. Have some sort of configuration option to set the user-agent for the InAppBrowser. This would allow a different user-agent from the main webview, but is also a more involved change.