When you put a PRB down the barrel after putting down a powder charge, the air in the barrel pushes through the powder, and out the vent, or flashchannel and nipple, blowing the nipple and vent clear. If they are blocked, you have a lot of pressure resisting that ball and its hard, if not impossible to load it. That is your cue that you need to clear the vent or nipple with a pick.
When you clean before loading, run just a slightly dampened clean patch down, in stages, backing it out, so that the patch is caught in the rings of the jag, until you reach the breechface. Then with draw the rod completely and pull out all the crud. Some will push forward and down to the breech. Now take a dry clean patch and run it down, again in stages, to pick up the black goo that is the crud pushed ahead of the first patch. The dry cotton will absorb moisture from the drud, and the stuff will stick to the patch and come out. If you think the barrel is still dirty, then run another patch down, but I recommend lightly dampening that third patch again with a little spit. Otherwise it might get stuck.
As to running anything down the barrel after the ball is seated, I know chunk gun shooters who run a lubed patch down the barrel after seating their ball. This lubes the barrel evenly, and increases the velocity about 1%. These guys are shooting for string measurments, and want to get that ball to the target as fast as possible so the wind can't blow it off center. As long as you have not primed the gun( put a cap on the nipple) and the hammer is in its half cock notch, I don't see how anything untoward can happen running a heavily lubed patch down the barrel after the ball.
However, after the ball is seated is NOT THE TIME to be cleaning the barrel. That i agree with. If the ball is seated on the powder charge, but you think that whatever crud in the barrel that you felt when loading will move your ball from point of aim, then fire the shot off into the backstop, clean the gun, and then reload.