Although a raw alternator produces AC, the alternator in your car has diodes which rectify it into DC. (I assume yours is a normal system.)
Therefore do you get DC from your alternator, or AC ? This is important because a transformer works on AC, not DC.
Since you have a transformer, it is efficient to step up 12V to 48V via a transformer. But you must apply AC. This can be done with a full H-bridge.
Your output spec is 144 W (48V x 3A). To provide this, you need to draw 12 A (average) from your battery. Add 15 percent to make up for losses.