Since AGM and flooded batteries are both the same chemistry (lead-acid) why would they not be completely interchangeable?
The AGM batteries can typically tolerate more aggressive current draw, but as far as charging goes, since they are the same chemistry I was under the understanding that a charger (or alternator) built for one will work fine on the other.
By and large it will work fine. An AGM battery fits inside the charging profile of a standard wet cell.
What a standard wet setup wont do is charge an AGM most effectively, but not so poorly as to kill it.
Im on 17 years using the same AGM charged with standard alternator.
Less internal resistance than a wet cell gives the AGM both superior charge and discharge profiles.
You can slam amps back into them at a much higher C rating for much longer before heat buildup becomes detrimental.