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I don't think alternator load is a problem with this kind of mod. The battery is only there to provide reserve power when the engine is off or when the accessories overwhelm the alternator, which is very rare. At all other times, the alternator pretty much puts out full voltage and powers everything in the car.
I think there may be a benefit to having normal electrolytic capacitors in a car, as the ripple from the alternator is substantial and you could smooth it out with capacitors, possibly improving efficiency? Depends on how the regulator circuit works, but if it doesn't measure RMS voltage correctly then this would be useful.
The way I see it, the primary use of ultracapacitors is to take load off the battery for starts as they have much higher power density than batteries.
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