Let\'s say I have a Cordova application with an id of com.StackOverflowExample.MyQuestion, which I created with Cordova 3 using the CLI (cordova create). I have
Yes, you can do that. There is more option for them, it's depends on how do you build your Android application (how do you create your apk).
If you create the apk using cordova, first you have to decode your apk:
apktool d .apk
e.g:
apktool d your.apk decodedir
Change the package="com.StackOverflowExample.MyQuestion" string in AndroidManifest.xml.
Encode your apk:
apktool b
e.g:
apktool b testdir/ your.repacked.apk
If you create the apk using any Android developer tools, you can change the id in the appropriate xml file (AndroidManifest.xml), and build the app.