I get where you're coming from. I may **** with my motors and build power with them but I always run as much of the emissions equip as I can. For me, my dog, and everyone behind me.
That said. US air quality has improved dramatically since the 70s. When manufacturers come and tell me they cannot make or sell me the product I want (truck with a manual) because that one particular option pollutes too much, I will get very pissed at this. I'm not even asking for diesel at this point. If someone drops a brand-new 2020 Gas truck that shifts with a stick I'd be first in line with my banker ready to buy it. But no, they emit too much.?
You mention the modern diesel trucks at 1000+ ft-lb torque being cleaner than the models before. This is very true, especially the new DEF systems. Is that fully because of the auto trans? No... Or is the engine capable of meeting emissions, but the manufacturer unwilling to sell one that meets a greater fuel economy standard?
Strict Federal standards for new vehicles are fine. My state does not run emissions tests anymore so I'm fine. But for the love of all that is good, don't pee down my neck and tell me it's raining. What isn't fine is telling me that choosing what gear my rig is in is bad and that I can't do it. These are dark times for those that like to row their own. I will buy dirty, sooty, oil-slobbering old trucks with a manual transmission before I buy a new one without.
Did you take your banker to the dealer and buy a Ram HD with a Cummins and manual trans before last year? You could've. But you probably didn't, and neither did anybody else so they cancelled them. If there were a strong enough business case for developing/testing/certifying a manual trans, then you'd see them available. Emissions are harder to get right consistently with a manual, and manuals really don't get any better fuel economy than autos anymore. Still, if there were enough demand for manuals, you'd still see them. The biggest reason that you don't, is money. There's not enough demand for them, so it's not worth it to the automakers to invest the time and capital. The fuel economy difference is neglibile or non existent, so there's very little advantage to a manual anymore unless you just like the control. The number of people that want to shift their own gears, just because, is growing smaller every day. Especially in something like a big truck. You can still get a manual in a Tacoma, but only 5% of the buyers actually go that route, and the numbers are worse for some of their other manual offerings:
https://www.tfltruck.com/2019/05/toyota-tells-us-exactly-how-many-manual-transmissions-it-sells-including-the-tacoma/
It costs an automaker tons of money to offer two kinds of transmissions in a vehicle. Like hundreds of millions of dollars. Time spent designing/testing/refining a trans/clutch system/shifter/PCM calibration, etc really makes an impact. You're probably paying a bunch of powertrain engineers 6 figures to do that stuff when they could be working on other things for the thousands of hours involved. Then, you have to test both transmissions for emissions (thousands of hours of development/cal tweaking and then official certification, all at several hundred $$ per hour), and you have to crash test both transmissions (A clutch pedal can really do some damage to a driver's lower body in an accident, potentially requiring alterations to the crash structure design). Then you have to manufacture/store a bunch more parts, and have more steps/machinery in the assembly process of both the driveline and the interior. That all costs money too. That's a ton of expense for a configuration that they're going to sell a couple thousand of per year with no additional profit over an auto trans to offset the development/manufacturing cost increase.
I have zero issue with a person doing their own manual conversion, or holding onto their older manual vehicle. Both are good options.