The simple answer to the OP's question is: you can use the start isolation wire or not bother. If you don't use the function, the ACR just doesn't isolate the start battery during the startup process... that's it.
While the instructions say to run the SI wire to the ignition switch where the solenoid wire is attached, it can be attached to the other end where it meets the solenoid on the starter itself. DO NOT attach the SI wire to the starter cable!!
The purpose of Start Isolation is to help protect sensitive electronic equipment
from surge and sags created in the starting circuit during startup. In order for the SI function to work
at all, your boat
must have separated Start and House circuits.
Some boat systems are wired through the basic 1,both,2,Off switch so that everything (electronics and starter) are always combined to the power source, regardless of the switch selection (Batt#1 or Both or Batt#2 powers everything). The SI function won't work
in this case so there's not much point in hooking it up. In my own setup, I've added in a second 1,Both,2,Off switch that allows me to power the House and Start loads separately. I can also use this switch for an emergency
jumpstart without using the fused House circuit and as an emergency
shut off in the start circuit.