The OTG is needed of the Due side for the exact same reason. The shorted pins tell the Due to go into host mode. If they aren’t shorted then it will be in slave mode.
The Host port on your Android devices are internally set, weather it’s a shorted pin or done in software it doesn’t matter, they’re always host.
You could use plug the Due into the host port and the Android. You would plug the large USB type A connector into the Android, and the micro end into the Due’s “Programming Port”. This will tell the Android device that the Due is a “USB Device” vs a “USB Accessory”. This is the feature @that_kidd wants and I have been working on implementing. It currently works, but not very well. You can try it and let me know, but it seems a lot of commands aren’t successfully sent between the two devices just yet.
So my recommendation is to stick with what you’ve got, OTG plugged into the Due which will use Android Accessory Mode.