However, I've been told if the wire isn't added to the ignition circuit, the second battery will not charge properly due to alt voltage fluctuations.
Not true.
When the voltage rises to 13.2v the ACR will tie the batteries. It will not untie them until the voltage drops to 12.8v. So as long as your voltage regulator keeps the voltage above 12.8v with the engine running, and they all do, the battery will charge.
Voltage does fluctuate. Most vehicle voltage regulators maintain voltage not as a precise setpoint, but within a range. For example my old Ford camper van holds 13.5v at idle, and 14.5v at any RPM above idle.
But that doesn't matter. The fully charged resting voltage of the battery will be between 12.7v-13.1v (depending on who made it). As long as the voltage remains above 12.8v the ACR solenoid will remain engaged and the battery will charge.
That aux start (or force tie) wire can't change any of that no matter if you hook it to start, don't hook it up at all or hook it to a switch to make it a manually activated force tie.
I was hoping if it could be taken off the 12v plug in the rear cargo area it would make life easy. But then again, if you're taking power from there, isn't it like taking it direct from the battery? I guess I am bit confused as to exactly what this wire controls on the units.
The unit is a dumb solenoid (a.k.a. relay). In high-voltage electrical it would commonly be called a contactor. There is a 12v electromagnet that draws less than an amp which pulls together a set of contacts which ties the big battery posts together.
To make the dumb solenoid into an ACR, they have added a small computer brain which reads voltage and automatically activates/deactivates the power to the electromagnet based on the voltage it reads.
The aux start wire is just a bypass. It feeds 12v to the electromagnet directly - bypassing the computer - to forcibly tie the batteries regardless of whatever the voltage is.
The high-zoot 500a ACR from Blue Sea has a 3-position switch - automatic (let the computer handle it), force tie, force untie (never tie).