I am pretty much in agreement with the Jim and Harry. There is no way break-in causes damage beyond what normal shooting of the same number of rounds does. Even firelapping, if you do it properly, doesn't pull out much metal. I've had occasion to firelap several military Garand barrels which had not been stress relieved before contouring, as modern barrels from good makers are. This resulted in a bore constriction under the asymmetric portion of the contour between the receiver and lower band, which, in addition to them being difficult to clean, was the reason for the firelapping.
Since I have a throat wear gauge, I was able to do before and after measurements. I also slugged the bores before and after. I found the throats moved forward about half a thousandth. That represents 1/20 of the military's allowable wear range of one hundredth of an inch, or about 150 shots worth of movement. Since there is no heat stress cracking associated with firelapping loads, and since a rough throat, as Tubb describes, can actually be made to shoot well again by polishing it forward after it loses accuracy, I don't feel this counts as real wear. It just means you have a half thousandth longer throat, which is not a big enough difference that you wouldn't see it between two match chambers.
The slugs showed the muzzles to have widened about one ten thousandth of an inch. The breech ends, about an inch forward of the throat came out about two ten thousandths wider than the muzzle. This was still smaller than the half thousandth breech-to-muzzle taper some consider desirable (though that is more for cast bullets shooting than jacketed bullets, which don't seem to care, in my experience).
My conclusion is that as long as you use a good method, such as Marshall Stanton's (Beartooth Bullets) or NECO's, and follow the instructions, firelapping will do no harm. I recommend you stay well clear of the cheapened knock-off of the NECO kit sold by Wheeler, however. Their instructions actually show a drawing of a poorly firelapped bore with the corners of the lands and grooves untouched and claim it is how the finished job should look. A recent Precision Shooting Magazine article described the kit being used on a .22 rimfire rifle and opening the bore up a whopping half a thousandth. That's way too much.
To reduce how easily copper sticks in your rust pits, I would fire a few firelapping rounds to dull the edges of the pits, then use Merrill Martin's method of wrapping a patch or two around the next caliber smaller bore brush (enough for a firm, snug fit in the bore) and loading the outside up with Remington 40X or JB Bore Compound or, my personal favorite, Iosso Bore Cleaner. These are all mild abrasives made of things like diatomaceous earth. They will blacken the patch with sub-optical microscopic metal particles as they polish down the offending surfaces and corners. None of this will remove enough metal to affect barrel life.
As to barrel break-in by alternating the firing of bullets with cleaning, I have always looked at this like stropping a razor blade. The softer material rubbing the harder one will be able to bend and fatigue away wire edges and the like. It is hard to imagine those being a major problem on a button rifled or a forged barrel or any lapped barrel? But break-in procedures have been around for an awfully long time. Back near WWII, even mass production rifle barrels were still cut rifled (AFAIK, and if all the WWII surplus rifling machines are any indication), but not hand lapped, as custom barrel blanks are. These barrels would have benefited most, I should think, from break-in. A broach cut barrel should, too.
The break-in may help burnish reamer marks on the throat, as suggested earlier, but I would use a very fine firelapping compound on a few firelapping rounds if that were my only objective. Or, as one fellow in a PS article was doing, attach stems to jacketed bullets and use them as rotating hand laps to match his throat to his bullet ogive perfectly.
