Try adding this to your config.xml file:
<config-file platform="android" parent="/manifest" mode="merge">
More info on the config-file element:
Know that setting the app to debuggable is a huge security risk, since Android is extremely lax when checking certificates in debug mode. I wouldn't ever suggest using an app with this flag set to debug in production.
I think you would be better served by diagnosing the certificate issue you're having -- that is, even if your root CA is trusted, the certificate itself seems to be rejected. Check the device logs for more information (adb logcat) to see if the cert is being rejected.
The following might help - it contains info on common certificate problems: