72 Swinger - Some wiring questions.

Now to figure out what that loose switched power coming out of the bulkhead should go to......
Likely its the power feed for the system.
Sometimes the design as shown in the service manual was executed slightly differently in production.
That might be even more true with a half year or an option.

I found that with my '67 instrument panel lighting & turn sig circuits. Rally dash redo

The service manual shows the standard harness used a welded junction in the '72 run circuit.
Reworking the NOx controller schematic as a simple add on to the standard harness, it would look like this:
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But apparently you're not seeing a piggypack by the ballast resistor.
So maybe Dodge had an engine harness made for Calif cars. Might have to do with assembly or routing issues, or could be a move to help production.

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As far removing, its your car to restore, repair, as you see fit. That is, within the rules you may have to comply with in Calif.
With the screw holes where the control unit mounted to the firewall - those would be worth plugging if the module is removed.