I'm no expert on ignition systems, so like usually happens, someone will probably come along after me with the correct answer and make me look like a dumbass. But being an electrical engineer (read Geek), I can't resist taking a stab at it.
The condenser is an old time term for a capacitor. The reason it is there across the points is that without it, when the points open, the coil will try to keep current flowing, so it causes an arc across the points. This can wear out the points really fast, or even weld them closed. The condenser charges up, allowing the current through the coil to flow for a short time while the points are opening, so that the points get further open before the condenser stops the current flow. This keeps the arc from happening. Then when the points close again, the points discharge the condenser so that they are ready for the next cycle.
So back to your question.... I would guess that the value of the condensor (capacitance value in Farads) is different between a 6 volt and a 12 volt system. It is a bit of a balancing act to get enough capacitance to prevent the arc from happening when the points open, versus too much capacitance that can cause an arc as the points close and the capacitor is discharged. The trick is to get just the right amount of capacitance to make the points live a long and happy life. I seem to remember back in the dark ages when all cars had points, that the real car guys would look at the points after a few thousand miles and could tell if they had too much capacitance or too little by which side of the points had the pit, and which side had the "tit".
So guessing here, but I'd say the right condenser is better than the wrong one, but the wrong one is way better than none. If your points last reasonably long, then you've got the right one.
Geeky enough for everyone?
Terry