Zuma,
Good for you tearing that base off to get that knot out. The old timers would tolerate them in the middle of the blade, but not in the base where they would mess up hafting. They would have done it just like you did.
Those knots are super common and super annoying in the Virginia quartzite I mostly knap. Most of the time you don't know they are there until you start sending flakes in and they won't go. Its like this little middle finger comes up out of the stone. As Chippinstuff says, the only way to get them (if they are small enough) is to send in a flake with enough energy to dive under the knot and scoop it out, leaving a pock mark or divot in the biface. And as he he mentions, sometimes the energy wave dives under the knot and keeps going all the way through the piece, snapping it. At least with brittle quartzite, more commonly the bending stress put on the thinner portions of the biface around the knot can't handle the stress load and the biface snaps.
Any way, I guess i'ts like all defects in the rock that turn up late in the process. You have to learn to pick your battles. When it's in the base like that, though, it's got to be blasted out!
Keith