I know both of the field technical guys in CA from school and both of them are very good with diesel diagnosis, so I doubt anything was missed if they came out to double check the diagnosis. Rail pressure is probably one of the first things that were looked at. If the rail pressure was close to the set pressure there is no need to cap off injectors.
You said you were running Bio at about 20%. Did you buy B20, or were you mixing B100 to get about 20%? In either case, you ignored the warning in your owner’s manual. That in itself would be hard to defend if you want to take them to court. At the training center in diesel class they used to have about 25 bottles of different fuels from all over the state, different brands, Ag, Bio, etc. and I don't recall any that smelled like "paint thinner". So are you sure about the quality of your source? That is one of the hazards of Bio fuels, there is no standard anyone has to adhere to. There are different ways to make it, and some ways are better than others. And some of the chemicals can be very corrosive.
I'm guessing that the injectors are stuck shut, and the reason the entire system is required to be replaced is Dodge is on the hook for a $12,000 engine. Whatever ruined the injectors is/will ruin the FCA, Pump, Cascade Overflow Valve, Pressure Relief valve, Pressure Sensor, etc. in time. When and to what extent is really unknown. And when those parts fail and it causes an injector to stick open and the piston melts, they are not going to be too happy. So if they have to stand behind it, they want a fully functional fuel system that has not been compromised. I can completely understand that position.
I see you have three choices, tow it out, pull the injectors and try to clean them up (assuming they aren't scored) and take your chance that is all that will ever go wrong. Or contact your insurance company, have them verify the fuel is not really #2 diesel and ask them to replace the fuel system, or step up and pay for the repair and move on with a warranty remaining.