I have done it both ways, with good results, but currently, based on the advice of shooters that are better than I (long list) I have opted for more clearance, .0025 to .003. In this range, a bullet will slip in the fired case.
When I am looking for a load (loading at the range, shooting carefully over flags) I start with a seating depth (usually into the rifling by an amount that experience tells me should be close) and start low, perhaps 27 grains, and shoot one shot per load, carefully, with .3 grain increases, until I can feel more effort opening the bolt than I like. I do all of this FL sizing for every loading. I take my time, and try to remember the condition that I shot the previous shots in. by looking at the target when you are finished, you should get some ideas as to where you should try to do some more work, refining the charge, and fiddling with very small differences in seating depth. As I understand it, for an average 6PPC, nodes are about 1.2 grains apart. so if you have paper between two shots that were fired quickly, in the same condition, you might try changing your load by a half grain or so, up or down, depending on where you are in relation to your maximum load ( as determined by test) Remember, as you come out of the rifling, even though you are still in to some degree, pressure is reduced, so you may have to change charge weight to get back to the same level of pressure, if that is what you want.