FWIW, I have dual EI on my RV-9, but no dual battery. The PMag models I installed self-power above the usual in-flight idle speed using an internal alternator, so even a total electrical failure wouldn't affect the ignitions until after landing. Unfortunately as I have had this since day 1, I can't provide any meaningful 'before and after' data, though if I were starting out today, I would go the full electronic ignition and electronic fuel injection route, and utilise a standby alternator on the vacuum pad to provide electrical redundancy. Some of these EFII systems allow you to meter fuel to the individual cylinder to perfectly match peak EGT for LOP operation, if that's your thing. They will also output a pulse-train to your digital fuel flow gauge/EMS to give you better accuracy than with a traditional sensor.
How difficult it would be to get an engineer to approve such an installation in a factory-built aircraft I have no idea. Probably "very"...