I'll throw in my 2 cents here. I'm a big fan of a dual battery system and no alternator (especially eliminating the rectifier area of the system). I've had good success running the secondary ignition system at 18 volts by using a Honda Minitrail 6V battery in series with the 12V power. At face value, this would seem to be a problem for the coils, but at high RPM the saturation (dwell) time is so short that the extra voltage only gets you back to typical lower RPM charge point. I was taught this trick by the guys running American Indy Racing Leage, who use it to make the Menards keep firing at very high boost levels and RPM (yes...they really do have a little Minitrail battery in the right side pod! even with a charging system). It is really helpful for the turbo guys, and is most important if you get a little lean at any point in the map. Make a big enough spark and you've got a fighting chance the burn will occur in the cylinder, instead of across the exhaust valve face.
If your ECM needs particular voltage range (typically a little under 12 to just under 16) you can series through an extra 1.5 to 3 volts to be sure of the system. All the control functions are running internal 5V limiters, it's just the speed of controllers and drivers that are looking for the solid 12V+. I hear that some of the stand alone systems are pretty sensitive to voltage drop, but I never had a problem with my Pectel system. If you run your injectors at higher voltage, they will absolutely snap open on time (they sure do close on time regardless of the voltage!....ever notice that!)
Keep in mind that your ECM looks (should- but not all do) at battery voltage to make injection duration adjustments. If your duty cycle is too far extended (beyond stock), the low voltage issues will really get you lean. You can separate the input voltage to trick a stock computer into adding time by feeding the injectors at 15-18 volts, but keep the ECM B+ (12-14V). You'll get fairly linear enrichment in the highest torque portion of your map/power curve (up there where the frequency starts to get close together).
Over the years, I've had problems with diode failures in charging systems that can take a battery down SOOO fast. It just seems like simpler is better, in this case. If you want to hold fuel pump voltage stable, independant of the ECM or secondary voltage, run the 12+6V and use a limiter to maintain exact pressure..... or....do like I did and run a separate battery for the pump (meaning I had 2 12Volt batteries and one 6 volt battery on the racer).
Kinda rambling on here...happens when it gets late at night and you start getting old. Regards, JimL