Selective incorporation is the process of expanding the application of the Bill of Rights to also include the states. It became necessary in order to guarantee people’s civil liberties equally across all states.
The two clauses together protect religious liberty but from opposite directions. The establishment clause prevents governments from having an official religion (thus giving all religions a chance to flourish), while the free exercise clause clearly empowers individuals to practice as they wish.
Someone accused of a crime may take a plea bargain because it reflects a clear path forward rather than the uncertainty of a trial. Typically plea bargains result in weaker punishments than does a court trial.
A right listed in the Bill of Rights is afforded clearer protection than one developed incrementally through court precedents.