Alpine, yes, they probably could, but how do you ever get the gear up then?
Suppose there is a too-high load on the main bus, so a relay is tripped and only the FADEC and a few essentials keep running. At what point do you decide to restore power to the main bus? And if you restore power to the main bus, the gear motor will start whirring away again, overloading the system anyway. And all the while you are flying with the gear partially hanging out. Not locked so you cannot land safely, but also not retracted so you incur a drag penalty with anything you do. Not good. OTOH, having your FADECS (all four of them in case of a DA-42) quit on you is also not a good thing.
I think there's no real solution to this problem other than ensuring that both alternators individually are up to the task of supplying enough current (by themselves) to power the gear motors. But that probably requires alternators that are too big/heavy compared to the average load they need to sustain. Remember that, although items like starter motors, gear motors and such draw a lot of current, they only run for a few seconds. So you can use the battery as a buffer. Unless its flat...
Hence the discussion between Thielert and Diamond on how to solve this. Apparently the "best" solution, given the circumstances, has been to modify the ground-power starting procedure in such a fashion that it is ensured that you never take off with a flat battery: Since you are now required (by the POH) to start the second engine on the aircraft battery (and not on the GPU), it apparently is assumed that if you're able to start that second engine, there's enough life left in the battery to power the gear motors too. Although, obviously, starting the second engine on the aircraft battery might just suck the last few electrons out of the battery anyway.
I personally still favour the solution chosen for the DA-40: an ECU backup battery which is, under normal circumstances, recharged by the alternator via the main bus. But if there is no power on the main bus and the engine master is on, a relay is tripped so that the ECU backup battery now powers ECU B. And there is a diode preventing other electrical consumers from ever using the juice in this ECU backup battery. But then again, I have no idea what the weight of this system is.