Running more than one battery charger, or a charger plus engine
alternator, will not damage anything. Each charger/regulator scales back it's output as the batteries charge based on it's internal settings. Two charging
sources will simply supply the aggregate of their output to the batteries. When the battery voltage rises to the predetermined level, each charger/regulator will scale back it's output.
With that said, most OEM engine
alternators don't include a smart regulator
, they simply hold the batteries at 14.2-14.4 volts the whole time they are operating. Even with these, a smart shorepower charger will not hurt anything (or get hurt).