If you follow the main power cables from your battery and 7-pin connector, you'll find they go straight to the disconnect and from there into the distribution system. Press the disconnect button and, as you found, the battery is effectively "disconnected" from the system, brakes included!
You are indeed correct...at no time should you pull the trailer "disconnected". While that seems a little obtuse at first, if it didn't completely disconnect (isolate) all 12v input, someone, either accidentally or intentionally, could activate the safety switch while your trailer is in storage. Shortly, you would return to a dead battery and potentially damaged brake magnets. "Disconnect", as you've found should only be used to truly "disconnect" your battery. It is a simpler method than physically removing the battery, but, the effect is the same.