That's the whole point to the add a battery pack. The charge loads from your alternator (or solar) run through the ACR. The very high loads of combined operation are handled by the switch, NOT the ACR.
Spend some quality time with the wiring diagram until you understand how the currents flow in the system. It;s simple and clean and a very good set up.
For DWH - The ACR with the add a battery kit is not the 350 or 500 amp magnetic latching relay you are thinking of. It''s a 120 amp charging relay that does not :combine".
The switch too, is different than what you are thinking. It isn't the 1/2/both/off of a traditional marine switch. Instead it switches both circuits of the charging system on or off, but keeps them separate from each other. But it also has a "combine" setting to combine both batteries. It's pretty cool but look at the wiring diagram. The settings are off/on/combine. The "on" setting is a single throw double pole switch, switching the battery circuits at the same time but independently. The ACR takes care of the combine to charge, but not the combine to self jump or winch.
In many ways, I think the Blue Sea add a battery kit is a superior way to wire up a dual battery system.
Anyway, hard to explain in words but easy if you look at the diagram.
https://www.bluesea.com/products/7650/Add-A-Battery_Kit_-_120A