The controller for your unit should be mounted separately to the air distribution box. It's hard to tell from the pictures you sent but if the wiring diagram you sent is correct for your unit then it's also showing it as a separate part from the rooftop unit.
The controller should have a connector sticking out of it like I have pictured below. Since your picture of the old rooftop unit has a bare wires I'm assuming they cut the connector off and just hardwired it, which is ok but a bit... view full answer...