There are really two types of isolators- diode and solenoid.
Diode Isolators use diodes on the charging system to isolate the alternator charge without tieing the batteries together through the charging wire. When you put any battery switch on "both"...it negates the diodes.
Solenoid isolators actually phisically interupt the circuit. However, once again, if you switch the batteries to "both", it will negate the isolator...
...unless Tom Brown wired it.
I also have the parallel solenoid you are talking about. All that does is tie the batteries in parallel fo a few seconds so you can start your engines. You could accomplish the same thing by running back and switching the Perko switch to "both".
With the parallel solenoid it completely eliminates the need for a manual battery switch that would tie the two engines together. Much easier also. My port battery bank runs the refrigerators and if I have been anchored out I will start the starboard engine first, turn the ignition on on the port and check the voltage, if it is low at all I will push the parallel switch just to not have low voltage to the starter brushes. Marine starters are expensive and love all the voltage they can get.