alternator output

Besides damaging the car's wiring, high current charging will heat the battery itself and can damage it, or at minimum boil off some off some of the acid. An alternator will supply its maximum output. On a stock alternator, running at idle, the output is limited by the low speed. It's possible your new alternator is putting out over 40 amps. Although its unlikely to hit the rating of 80 amps at idle speed, it will get there at even normal driving rpms. If the battery is very low, its best to charge it from a charger, and control the rate of charging.
Here's a series of photos showing a low battery drawing current from a battery charger.
Alternator amp rating.