There is no harm in connecting in a parallel battery. It's no different than suddenly having a larger battery.
Using a battery switch that has a field disconnect only works if you have an externally regulated alternator, as far as I know.
Battery switches are very simple devices. The chances that it will fail in a way that disables the make-before-break connection and does not completely disable the switch all together is extremely remote. If you worry about this possibility I would say you take much much bigger personal risks setting foot on a boat in the first place than you do putting your alternator at risk by switching batteries while the motor is running.