Some nice suggestions Eldanesh.
According to my suggestion it would be 21 per turn at 3001 points.
for every 1000 points, or part.
So if you're playing 1000 points, then it would be still only 1d6
1001-2000 would be 2d6
2001-etc.
It accounts for the fact that people generally play 500, 750, 1000, (and then jump to) 1500, 2000 point games. Only really removing 3d6 in very large games, when people are playing with upwards of 3000 points.
However I could see adding a modifier to the roll depending on the points value of the game. Like D6+x (for every 1000 points or something)
I don't think that rolling randomly for each marker is a good idea, as it removes a certain little 'tactic' to the game of where you leave BMs.