Every sanded down a pine board so smooth only when you apply a stain it roughs up? The water or liquid caused the grains to swell up and bulge out. This is why intermediate sanding is required after each coat to smooth out these rough areas.
Yes, paint and more paint will cause these rough spots to be smoothed out. The paint actually gets in the valleys and makes it smooth.
Cedar shingles are the worlds worse at doing this because on a humid day, they will soak up moisture and do this anyway.
Yes a good primer and a good paint would have slowed down this process, but it is almost natural.