It's generally a bad idea to ignorantly hook up a charge controller to an alternator/generator because the short circuit amps on an alternator/generator can be many times that of what it is rated for, unlike PV. Also, it has inductance that can spike many times the voltage. Both of those things could easily result in a current or voltage way outside spec of components on the input stage of a charge controller.
The ideal would be to have a charge controller measure the effective output of an alternator/generator into a battery, and vary the exciter field current to reach the constant current or constant voltage part of a charge curve. This probably wouldn't be too hard to put a prototypish something together with all these off the shelf embedded boards these days.