Yes, there were a lot of different powder charges to produce different velocities. Only those with the smaller charges needed the cotton filler to hold the charge near the primer to ensure consistent ignition.
The reason for the different velocities - they were intended to simulate different yardages. That way, all of the cartridges could be fired at one distance, say 200 yards, but the velocity would be the same as a full-power load fired, at say, 500 yards, or 1000 yards, etc. If the armor or glass plate was designed to stop an AP bullet at 500 yards you simply had to fire the appropriate test round at the shorter distance to see the results. So, the purpose was not to find what loading pierces the plate at a certain range but to see if the plate stops a bullet at a certain range. Same ting, only different.
Not perfect but ingenious, eh?