I think mounting the solar panel(s) inside the car would work fine. (sitting in the rear hatch etc). From my understanding silicon solar panels get their energy from the visible spectrum so the UV block in the glass shouldn't really hurt anything.
Thinking about this more... perhaps the way to go is really simple. Use a regular grid charger, which is useful to have anyway. When you have no access to electricity to plug into, simply plug it into an small inverter (cheap!). That inverter would be tied into the 12 volt battery through a charge relay such as they sell for marine applications. The charge relay would only activate the inverter when the voltage is above a set point and disconnect when the voltage is low.
Then, use a cheap solar panel sitting in the back to charge the 12 volt battery. Say 15 watts, $80 from Northern Tool.
In operation, the 15 watt panel is not enough to keep the grid charger running full time. So the system would cycle. The panel would charge the 12 volt battery. Once the battery was fully charged, the voltage would go above 13.0 volts and the relay would engage, activating the grid charger. The grid charger would operate for a while, draining the battery below 12.75 volts and turning itself off. This cycle would repeat.
Such a system would keep both the 12 volt and hybrid battery in good shape even if the car was parked for a long time and is (relatively) cheap. Probably not enough to "balance" the pack but you could always just plug in your grid charger for that.
Figure $250 for the grid charger or $100 if you make it yourself. $80 for the panel, $80 for the ACR relay from Blue Sea Systems, $40 for the inverter. The system could keep both the 12 volt and hybrid battery in good shape even when parked for long periods of time.
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