Not an expert, but here's my understanding from reading about this over the years ...
Both options are good for players who (a) believe they have potential, but weren't getting any/quality scholarship offers, or (b) have academic issues that prevent their admission. In both cases, the Prep or JUCO route gives them an opportunity to improve football and academic qualifications.
The Prep School route is similar additional high school. It has the advantage that the player does not lose NCAA eligibility, and he can be re-recruited the next year and/or enter college when he's ready. The disadvantage is that the student pays his own way.
The Junior College route is not much different than an NCAA 4-year school. The advantages are that the student can get a scholarship at the JUCO while working to improve football and academic credentials. The disadvantage is that the "5 years to play 4" begins ticking and the player will typically be locked in there 2 years, or until he gets his degree.