That doesn't sound right at all. The factory integrated trailer brake controller is already wired up and ready to use. If he connects the existing wires under the dash to a power source, that's just a waste of time, might be an electrical/fire hazard too.
The wire in your photo are this post, the one connected to the right post is the wiring to power your trailer through your factory 7-pin connector. This was previously wrapped up under the brake booster as I described earlier. All that extra stuff running off the other battery, I have no idea.
@intheburbs