It’s a good question. A couple things come to mind, but I don’t have answers, just more questions.
Pressure curve, already mentioned, was the first. This may interact with the harmonics of the barrel or some such idea.
Also, I would think that the amount of fouling different powder brands or granulation, or both, create will result in a difference in velocity spread. In other words, less fouling could/should result in less velocity variation in a multiple shot string, right?
If I may be allowed to mention black powder cartridge rifle shooting in order to bring up a point related to the question (moderators?). In Paul Matthews book on black powder cartridge rifle shooting, he suspects that powders made in the latter half of the 19th century left fouling that was more moist than modern powder. He pulled some powder from antique cartridges and reloaded them and shot them to analyze the performance and fouling. Thus, it was easier to clear (as in when you ram the next patched ball down), as opposed to dried / baked on fouling that is hard to remove.
The point here, is that different granulation of powder and different brands may leave differing amounts of fouling, and differing qualities of fouling, which I suspect will have an effect on the velocity spread of a string of shots.
No answers, but possible reasons that these things matter.
Norm.