We had a chat with our hardware engineer about this. Gist is that it should work but to be careful about inrush current.
Here’s his message:
He says that he will put the USB circuitry on a separate board. If that is the case, then, yes use the System Vin pins. But - he must be aware of the inrush current at turn-on that the super caps will present to the USB. It would be best if he were to create a power supply to provide the System Vin which has the super caps on the output of that power supply. This topology would limit the inrush current, and would provide the hold-up during transmission.
Other concern: are you attempting to transmit a message while it’s shutting down? That would spike the power draw and may end up draining the caps before it’s complete.
Also, we were wondering, how will the Dash know that main power has gone away in order to do the housekeeping things?