Forgive me if I'm misinterpreting your post, but as I'm reading it you seem to be thinking of State of Charge as just whether or not the battery is being charged. SOC is rather a snapshot of the current charge level - is it 40%, 80%, etc. That can be estimated via voltage level, or determined more accurately by measuring the current flow with a meter (hall meter or a shunt). If you're using a current meter, you obviously want to know everything going in and out of the battery - if you don't, then what's the point? So no, you don't want to bypass the sensor by connecting things directly to the battery without going through it. That said, I doubt that most accessory usage will have a large impact on those calculations, so doing so probably isn't going to mean much. However, if you're bypassing the sensor with a large amperage draw, or perhaps a lengthy one, then obviously the actual and calculated SOC of the battery are going to diverge. What happens then I can't say - perhaps an engine light if the truck senses a battery voltage that's lower than what it should be per the calculated SOC? I doubt you're getting stranded, but maybe it's possible in an extreme situation.
Regardless, it's easy to just connect your grounds to the chassis and then you don't have to worry about it. Easier anyway. As to why Ford only measures the current on the primary battery, I suspect it's because they just don't care all that much about the secondary. That is, if you take care of the primary's charge level, the secondary will follow along well enough. Unless it's gone bad - I've had that happen with a bank of LFP house batteries where half of them were unknowingly damaged and I went a night without power despite my trusty Victron kit insisting I was at 60%.
I suspect, too, that ford doesn't care too much about absolute accuracy on this front, since they have to account for external charges and drains anyway. I mean, if someone connects a battery maintainer to the terminals, the sensor obviously isn't picking that up, nor if someone did the same with a portable winch or something. So maybe the truck may not get all that upset when the SOC isn't what it thinks.
Still, why tempt fate.
Glad to see you understand State of Charge, your first two lines are correct up to "or determined more accurately by measuring the current flow with a meter (hall meter or a shunt)" You also make goods points elsewhere and spot on about batteries in parallel, one can be bad, and you wouldn't necessarily know it. (Please read to the end, more surprising info.)
Not to get too far off subject here, the question is: can a ground wire be hooked up to the battery post in lieu of the chassis? The answer is unequivocally yes. If this weren't true, the second battery would not be connected directly to ground via the engine block, and they wouldn't have put studs on the battery connectors for optional connections. Current is drawn by any accessory equally from both batteries. (More on the current sensor below)
The rest of the story for the curious:
SOC is the state of the batteries at any given time. SOC is a battery indicator, not a condition of operation per-se. You are also correct, the system monitors voltage to determine SOC, not current. If you ever have a DTC or fault, the first rule of order is to check the SOC of the battery. Where I think we're getting off track here is confusing SOC with how the current sensor works and its purpose. The current sensor cannot measure a State of Charge, only whether the alt/gen is functioning properly to bring the SOC back to normal. (More on this later) It's also possible that the system can detect a sudden or higher than normal draw and trigger a DTC via the current sensor, but that would not make sense since it would also be drawing from the second battery as well and not monitored.
From the manual:
Charging System Warning Indicator
The charging system warning indicator is controlled by the IPC based upon the battery low state of charge message received from the GWM over
the HS-CAN3. The GWM receives the battery low state of charge message from the BCM over the HS-CAN1. When a fault is detected in the
charging system, the BCM sends the IPC the battery low
state of charge message to illuminate the
charging system warning indicator.
Battery Current Sensor
The battery current sensor which only monitors current flow in/out of the battery, The battery current sensor is attached to the battery negative
cable. It is supplied a 5-volt reference voltage and a ground from the BCM. The battery current sensor is a Hall-effect sensor that supplies an
analog feedback signal to the BCM. The BCM reads the battery current sensor feedback voltage to determine how much current is flowing
through the battery ground cable.
The BCM uses this information for battery state of charge. (See next paragraph after the acronym descriptions for hypothetical conditions.)
A whole herd of acronyms to say the computers are monitoring the charge state.
battery energy control module (BECM); parameter identification (PID); Diagnostic Trouble Codes (DTCs); Body control module (BCM); IPC: Independent Plausibility Checker; GWM Gateway module; CAN- Many types, system communication buses.
What if:
What if the current sensor was actually used in the shutdown scheme. How would it work? If you had a 1-million-amp hour battery, and continuously drew 100 amps, the state of charge would take a long time to change. Voltage levels would remain stable for many hours and whatever you were operating would continue to run. However, if you had a 100 amp-hour battery with 100A draw, it would instantly change and the BCM would try to shut the system off, you may get a DTC code. The Hall device would sense 100A draw in either condition. It would not set this as a condition to shut down, it would determine the voltage drop or SOC as the condition to shut down. It wouldn't care how much current is drawn, but rather how good is the State of Charge as it is being drawn down. A Hall sensor can only detect current, not voltage. As the battery goes down in voltage, the computers would respond to the voltage change, not the current change.
In the old days, battery/charging systems measurement was accomplished through a shunt (as you also mentioned), the meter could show both negative and positive current on an analog scale. It was simple to look at the meter while running to determine if the battery was taking a charge. (Or at least the alternator was generating enough voltage to charge the battery)
When the vehicle was off and a load applied, (headlights) it always read negative. The human was the computer to determine its health.
Today technology is leaps and bounds past those days. The Hall sensor is a very efficient way to measure current via a FET circuit, drawing virtually no current to operate and no loss through a shunt. If a load is turned on and the battery drops to a given level, things start to shut off. It doesn't matter where the source is drawing from, the battery (or batteries) will still go low, and the multitude of sensing points will pick that up. These trucks are quite literally a computer on wheels.
There are countless times the SOC terminology is called out in the troubleshooting guide as a condition of the DTC, not being a DTC itself. If there was a short, then you would get a DTC, again, first order of troubleshooting in most all cases of a voltage related DTC, is to check the batteries for connections, shorted wires. SOC, etc. It doesn't have to be sensed through the current sensor; it's monitored via voltage by the BECM/BCM...
Your last couple of paragraphs are perfect timing as to my next point and reason for another upgrade to the truck, two batteries are on order, will have them tomorrow. Why? My original batteries have been on a maintainer for a while now simply because 6 months ago, I knew they were near the end of their lives (Corrosion) and I don't drive it that often. (Sadly) Yesterday I went out to check on the state, popped the hood, and there it was. A battery symbol on the charger/maintainer with a red X through it. Why? The manual says, " battery will not hold charge". So, I checked them manually, the driver's side battery is toast. Ironically, the truck starts and runs normal and NO DTCs.
The Noco is smarter than the truck computers. 
Sorry for the long-winded reply.
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