The <supports-screens/> tag is not a valid tag in config.xml. That's probably why you are seeing the same tag in both, as the build service is ignoring it.
As for how you fix it. Currently you can't but the next release of cordova-android will include the ability to add a <edit-config/> tag which you will be able to use like this:
<edit-config file="AndroidManifest.xml" target="/manifest/supports-screens" mode="merge">
<supports-screens android:smallScreens="false" android:normalScreens="false" />