Those are marketing terms, not real world numbers. What it means is that a "12v Panel" can produce enough voltage to charge a 12v battery, but not enough to do a 24v battery. Likewise a "48v Panel" will produce enough voltage to charge a 48v battery, or a 24v, or a 12v. When you're calculating for your SCC the only time those numbers really come into play is if you're using a cheapie PWM controller. Since the PWM controllers just clip voltage to whatever battery voltage is, going over that is a waste of energy.
For example, if you've got a little 12v panel on a 12v PWM controller and a 12v battery, the panel is probably producing 18-ish volts and the PWM is just clipping that down to the 13.5-ish that your battery uses. Anything between that 13.5 and 18 is just dumped/wasted. If you were to throw a 48v 300w panel on a 12v PWM and battery, that's anything between 13.5 and 60v that's just wasted and only 5 amps going into your battery (and probably fried your little controller in the process anyways!
). That's where the whole 12v/24v/48v panel thing really comes into play and your panel, PWM, and battery all need to be in the same range.
Now, let's say that your little PWM just wasn't able to handle those "48v" panels your friend gave you for your birthday and you went and picked yourself up a decent little MPPT controller. Now things start getting good! The MPPT controller is trying to do all its battery math by watts, so your fancy 48v 300w panel is pumping 60v into the controller. The controller knows it's a 12v battery, so it's going to take the extra voltage and convert it to amperage. Now that 5a @ 60v is coming into the MPPT and it's being converted to 25a @ 12v of charging going to the battery. That's a helluva improvement! Since the MPPT can actually USE the excess voltage you gain a LOT more efficiency out of it.
Tl;Dr: PWM Volts In = Volts Out panel amps, MPPT Watts In = Watts Out, total amps.
*Just as a rough reference guide guys, I know it's a bit more technical than that.