I have also commented it at stackoverflow http://stackoverflow.com/questions/27773143/can-i-remove-this-permission-it-cause-install-failed-duplicate-permission-in-a#comment60224461_27773143
I faced the same issue with one of common cordova plugins. I understand, you have solved your issue but just in case others want to know the solution.
Use ${applicationId} instead of actual name in androidmanifest.
