I am not sure I understand your question fully, but here are some elements of answer:
-Native extensiosn have an issue with java libraries, it might also be a problem with aidl files : AIR 3 Native Extensions for Android - Can I/How to include 3rd party libraries?
-About the manifest additions, you can modify the manifest of the final apk this way :
Go to NAMEOFYOURAPP-app.xml
After :
<!--The suppression of android.permission.INTERNET will prevent you from debugging.-->
<uses-permission android:name="android.permission.INTERNET"/>
You can add permissions
After :
<![CDATA[
<manifest android:installLocation="auto">
You can add activities and services.
In your case, instead of :
<application android:enabled="true">
<activity android:excludeFromRecents="false">
<intent-filter>
<action android:name="android.intent.action.MAIN"/>
<category android:name="android.intent.category.LAUNCHER"/>
</intent-filter>
</activity>
</application>
Write :
<application android:enabled="true">
<activity android:excludeFromRecents="false">
<intent-filter>
<action android:name="android.intent.action.MAIN"/>
<category android:name="android.intent.category.LAUNCHER"/>
</intent-filter>
</activity>
<service android:name="BillingService" />
<receiver android:name="BillingReceiver">
<intent-filter>
<action android:name="com.android.vending.billing.IN_APP_NOTIFY" />
<action android:name="com.android.vending.billing.RESPONSE_CODE" />
<action android:name="com.android.vending.billing.PURCHASE_STATE_CHANGED" />
</intent-filter>
</receiver>
</application>
But for your applicaiton to work, you still have to fix some .jar problems (as states above)