Hi Kurt,
First, don't worry about the lock mortise breaking into the barrel channel by the upper leaf of the mainspring. This is common and is because lock makers do not position that upper leaf low enough on the lock plate to accommodate a barrel with a large breech. Even if it did not break through, the residual wood is usually paper thin. Many original guns and high quality contemporary guns have that feature. With respect to staining, if you are using an acid based stain such as aqua fortis, vinegroon, or even dissolved ferric nitrate, there may be some risk of the acid base reacting with the metal. If the stain is blushed with heat as it should and then neutralized with baking soda in water, or ammonia, or lye dissolved in water, there should be no acidity left to cause problems. Moreover, if you seal those spaces with finish, you should have no worries. However, if you stain and/or finish those mortises, the wood may swell and the parts no longer fit without scraping away wood. So it is a gamble. I seal those spaces but have to scrape away swelled wood others don't but then have no protection from moisture in those spaces. You can find plenty of original guns with unstained or sealed mortises that survived several centuries in pretty good shape. I have several originals that had finish applied to the mortises and they are just fine too.
dave