I have two C-40's used on solar setups as charge controllers, and I would second Roy's assessment. For alternator inputs I would almost be surprised if the impure DC played havoc on the C-40's charging alogrithms.
Mine don't agree with each other on voltage, and they only have a .4 volt resolution. The amp resolution must start at 1 amp as I don't ever recall seeing anything between zero and one. I have specifically observed that the bank was charging even when the C40 meter read zero Amps. I have a shunt in series with it and an analog amp meter, which I like much better. Aside from the Amp hour meter function, which is why mine are still connected, but which I doubt is extremely precise, I much prefer my old fashioned analog guages.
One additional note is that I had used one of my C-40's as a diversion load in the past and found that it was slow to respond when using a larger diversion load with a smaller battery bank, allowing the bank to discharge more than I intended. This was a 48V bank with an actual capacity of about 50 Amp hours and a 900 Watt diversion load. From what I have read of others experiences, this appears to not be a unique result. I suspect that the diversion load alogrithm behaves more acceptably for larger battery banks relative to the diversion load size. Rich