Interesting suggestion... if you're providing the boost in voltage via buck converter, you could wire the brake switch to disconnect it so the alternator sees battery voltage and turns back on. You'd get regen back into the battery whenever you tap the brakes. The only downside is the alternator would stay on while you're stopped with your foot on the brake.
If instead you could signal the buck converter to disable whenever the car goes open loop, that would be even better. It would go open loop when DFCO and charge the battery, and then re-enable the buck converter once it goes closed loop at a stop.
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