I'm using Quickload, Ver, 3.6. Over nine years that I've been using it, I have yet to find a significant error in its' database, but there's always the possibility.
QL defaults to a 400 grain bullet. That might be wrong. I have never played with the .40-82 myself, so have no other data.
It shows a maximum case volume of 79 grains of water, or 5.129 cc. Can you measure and verify? If that needs correcting I can do it and re-run the models.
Quick troll thru the Innertubes got me this URL
https://winchestercollector.org/foru...eloading+data/
There the posters are saying AA5744 and 4198, with bullets around your weight. I have burned a lot of both in .30 and .35 caliber cartridges, but with gas checked bullets at 1600-1800 fps. Still, if you can get them, would be worth a try. Mike Venturino was very big on 5744 for large cases. I did not get good consistency until I got it up to 18-20,000 psi, however. 4198 is said to perform at lower pressures, but I have no quantitative data for large cases. It is one of the default powders for the much smaller .22 Lovell, which a pet of mine, and the .222 Remington. But there we are hammering jacketed bullet out the muzzle at 2700-3000 fps, pressures 40-45,000 psi. When I did reduced loads in the .222, I used Red Dot. Do not try that in your .40-82.
I object to cornmeal type fillers because they raise pressures, sometimes by a lot. That may however explain how you found loads using 3031 with a filler. The filler could/would have pushed the pressure into the range that 3013 likes.
I hold no brief whatever for Pyrodex in any form, because it deteriorates with age. I haven't shot black for a number of years now, but when I did I went to great lengths to obtain Swiss. 2F would be the right granulation of Goex. 3 to 5 grains of any sort of pistol powder, then fill the case with your black. Do not weigh, just fill the case to the base of the bullet.
Generally speaking, plain base bullets will start leading the barrel at about 1500 fps, unless cast pretty hard. No permanent damage, though. Many years ago I shot hundreds of commercial "hard cast" .35 caliber pistol bullets through my Dad's .35 Remington. They were miserable until I learned to push 'em to 1800 fps with XMP5744. I don't know how hard they actually were, but today I'd guess Br 15 to 18.