You pay by the (kilo)watt-hour. It does not matter if the load is 12 volts or 120. If it is 50 watts then that is the load.

The 50 watt/12 volt light bulb will draw 50/12 = 4.17 amps. That is from a 12 volt transformer. That transformer will draw (less losses) .417 amps from the 120 v lines.

A 50 watt/120 volt bulb draws 50/120 = .417 amps.

Where you MIGHT save some power is that with MR-16 bulbs is that you can more often place the light more specifically where you want it. And thus need less total wattage.

But you can get MR-16's in both 12 and 120 volt version.

But 12 bulbs and fixtures are more common.

If you really want to save power then get CFL's.