The Mega should already recognise the full 128 pins in the App settings by default.
In fact, just pick the Generic Board in the App and then using the define command in the sketch you should have no problems using all 128 vPins on any Arduino board.
The device setting in the app really only changes how it interprets the direct pin control in the App (Analog & Digital)… when using only Virtual Pins (in the App) and code, the device type becomes irrelevant (aside from showing all 128 vPins that is)