Re: Battery isolator "Can I get rid of it"?
There are switches that are not make before break. Note that make before brake can also cause problems. Example you have one fully charged starting battery and one totally dead trolling motor battery. When you turn that switch what you have is a small wellder. You have big heavy cables coming to the switch and when you turn the switch and it makes the next battery it is almost the same hooking cables up backwards. You have current flow 2 or threes times what your starter draws and it can warp the contacts, or weld them together.
I personally like battery Isolator for charging 2 batteries. With a battery isolator a switch that does not make before break is best. With the isolator you can turn anytime and even thru off and it will not hurt your alternator.
Also even if one battery is totally shorted and you have to disconnect to stop the wires from burning you can still run your gear on the second battery circuit while the motor is running if you have a good alternator. Must make sure the positive battery terminal is taped up and protected from shorting to ground. The other battery will protect the alternator and voltage regulator. The isolator will feed the same voltage to the dead batteries terminals and every thing connected to them.
There is no perfect system as some are better for your use and some better for my use. The key is to understand the options and pick the one that works best for you.