I have no doubt in my mind that part quality has dropped significantly in the last 12-24mnths but I have to ask, how you are taking these runout measurements? I can't think of a procedure that would give accurate and repeatable results without investing in some serious equipment.
All you need is a dial gauge and set the crank on #1 & #7 journals. I don't have v blocks that big, so I'm using the block and a new bearing shell in 1&7 only so the rest of the journals can spin free and clear. Not as convenient as working in the open, but it gives repeatable results. I used my new dial gauge with .0001" increments to double check, and found that there's about a .0002" margin of error (which means my rear seal runout is still over .0006" out of spec). If you don't have a upside down block, I imagine you could always cut some v blocks out of hard wood.
The crank is kind of W-shaped, which looks weird when plotted on Cummin's chart since it's has a slight twist as well. I wrote down my first plot, and was getting 5" readings, so had to re-do my measurements and clock it all again. I found my o'clock by marking on the journal when the dial indicator started to rise and hit .001", then whatever max reading, then back down to .001" so that I could pick the right clock "time" in the middle. Lots of room for error, or for a non computer controlled inspection to fudge the numbers. Looking at the crank straight down with my sharpie marks on the journals, it's kind of
~-___---""---___-~
2, 0, 2, 3, 3, 2, 0, 2
^ front oil seal
^#1
^#2, etc.
1 & 7 are always zero (if they're not, then the journal is egg shaped).
Now, I know pretty much nothing about manufacturing a crankshaft (or thousands), but just with my small sample, I'd say it's pretty common (At least with ISX cranks) to get them imperfect, which would be why it's fairly common to find new engines with different sized bearings due to regrinding of the crank.
a crank just sitting in a wooden shipping crate will easily (given its weight and size) be out of spec from end to end by 0.0008" or more, until it has had some run time on it in a more precision environment (the engine block) .. simply because it is suspended by wood, etc.. in the crate, due to settling in the box. I went thru this same type of issues, and measurements, when shipping precision-made machinery from USA to europe in the past. Unless that shipping container has some seriously rigid steel retainers.. it is impossible for that crank to be perfect .. even after an hour is settling.. nonetheless weeks or months and being tossed around by the yankes that carelessly delivered it.
I don't have micrometers big enough to measure the oil seal ends, unfortunately. I'm hoping that your theory is right, and it does sound plausible and fits with the way it was shipped. 2 chunks of styrofoam supporting the ends, crank in a bag, and tossed loosely into a box made of OSB. The measured "high" points on the ends were facing up.
Compared to the way the aftermarket crank I got a few years ago was shipped, it's kind of appalling lol.
All of that said, I'm sure that the last crank WOULD have caused me issues. It even made polished spots on main bearings 1, 4, & 7 due to the U shaped .010" bend. With everything new, I'm betting plastigauge shows .002-.003" clearances, which is my next step before it gets it's final bolt in and flipped over for pistons.
I've read that crank ends under high torque has a lot of bend and twist, up to .050" Again, an area I really don't know much about, which is why I've been relying on Quickserve to check everything.
I stumbled across this video, and ended up being fascinated by this guy repairing a broken crank, while wearing flip flops and working on a dirt floor.