Yes. Those are the holes where the shifter will mount.
Concerning shift knobs, they aren't meant to come off. They are NOT threaded on like most others. They are molded on over splines and a lip. Careful application of heat might soften them enough to be removed. But, best thing is to just leave them on.
On my first F150 ('88 4x4), the main shift knob eventually got loose to the point where I could spin it and feel the splines inside slipping. But it never did come off. Also, the little disc with the shift pattern on it will get loose and rattle and spin as you drive down the road. But it's held in a deep groove and won't come out easy either.