This is something that looks no “Too difficult” to perform…
I mean, the flux software already have “Stop on this specific layer”.
Why not use this function to activate any specific output to run a second motor/feeder??
The “Y Connector” that @Jimustanguitar mention could be pretty close to the extruder and make the inlet hole of the extruder a litter bigger (if necessary).
The only issue here, cold be a mix of color in the first printed layer after the 2nd motor is activated (in order to fill the 2nd material), but this can be a short part of the printed part (depending of how far the Y connector is in relation with the extruder’s tip).
Also, this can be fixed by indexing some material before start to print again the piece.
Or… make a little line the one that the FluxDelta make sometimes when start a new printing on it.