As many others have noted, Peterson no longer dip stains. Occasionally, you might see a bit of bleed at the top of the mortise, but nothing like when they dip stained. You might also see some dark areas in the mortise from the drilling process, which some pieces of wood are more prone to. I imagine that it would be most common in the system pipes because they simultaneously drill the mortise and moisture well and shape the shoulder on the lathe, so the bit is spinning inside the mortise for quite awhile.
Regarding the pit, it was of very little concern from a durability standpoint. Pits are almost always quite shallow and rarely more than a small fraction of the thickness of the wall.
One of the first steps in Peterson's manufacturing process is to sort the preshaped stummels by which finish they will receive. Each stummel is carefully examined, both dry and wet, for grain, color and flaws, like pits. The stummels with the most flaws or pits are graded for rustication. This doesn't mean that rusticated pipes are bad or are more likely to burn out. It's just a practical way to use that piece of briar and prevent it from going to waste, keeping the cost of all the pipes they sell to a minimum. Peterson's rustication process actually makes it one of the most expensive finishes for them to manufacture. IIRC, it takes an average of six minutes of to rusticate a pipe.
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Since yours is a rusticated pipe, it's no surprise that there was a pit inside the tobacco chamber. Yes, this is one reason that manufacturers use bowl coatings --to hide inconsequential flaws. That, and even more importantly, to protect the bowl during the break-in period. The truth is, there could be a pit inside the chamber of a smooth Supreme-grade, too.
So, while your concern was understandable, in the future, don't let it worry you. I'm glad the good folks at Smokingpipes took care of your concern and that in the end you love your pipe. Happy smokes!
