I'm well acquainted with the process for centerfire rifles, but hadn't considered that it might (and probably logically, too) be more extreme for muzzleloaders. With CF rifles there are changes in trajectory, but it takes a lot of elevation change to cause the kind of differences you cite. With the slower and less airworthy projectives from MLs, it only makes sense that they would be affected more, especially as range stretches and velocity gets really low. While I've hunted as high as 12,000 feet with a CF rifle, my top with a ML is only about 2,300 feet. I'm sighting and doing most of my shooting at sea level, BTW. Since I rarely shoot more than about 50 yards with a ML by choice, I haven't noticed any change between 0 and 2,300 feet.
But based on your reports, I'll be watching for significant change in trajectory if I start pushing 100 yards or beyond. I'm not likely to shoot so far, but you've provided very useful info for my "data base."