College baseball is very unique because some of the best talent in America will sign with an MLB team right out of high school. You’ll also find some of the best players who don’t opt to sign professionally out of high school instead will play at a JUCO and then sign after they’re drafted again. This is really driven by the athlete’s desire for flexibility for MLB draft eligibility while also being able to keep the option of transferring into a 4 year school.
So to say that all the best players go D1 right away would be inaccurate; the best players are spread around D1, JUCO and the other levels to some degree as well. You’ll also see more transferring in baseball than many other sports, it’s a commonly accepted practice.