Good stock wood does not grow on trees. A bark inclusion almost always has to be cut out, and a plug made to tightly fit the hole. Lots of European guns have them, as they are made from highly figured wood and a lot of stump wood, where the tree grows in swirling and twisting ways. I have never hesitated to use such a blank, and do not mind the obvious repair. If the rest of the gun is architecturally sound, the "blemish" does not detract from beauty or worth of the piece. Mike Brookes posted some images of a wormy rifle he made some years ago, and I thought it was so cool and full of character. And I've seen stocks that were outstanding that had a mineral deposit and were marked down in price as seconds. Such a deal for the builder who can see past the dark slash or blotch.
As far as the structural integrity of the stock, I don't think that the patched stock can tell the difference. In a longbow, if there is a crumbly knot in the working limb, it is simply cut out, and a "dutchman" glued in, and the bow is happy. And a bow's wood does a lot more actual work that a rifle stock.
