When Jefferson established the University of Virginia, rather than “secular,” he wanted it to be “nondenominational” not restricted to a specific Christian denomination. Until then, other universities (Harvard, Yale, William & Mary) were established to train pastors of a specific denomination. Jefferson invited all denominations to establish divinity schools on campus so students could choose which they wanted to study under and to fellowship in a broader Christian setting.
Regarding Jefferson writing the Bill of Rights or U.S. Constitution, he was out of the country when they were written.
Regarding the 1979 Virginia Statute of Religious Freedom, the act was to establish “denominational nonpreferentialism” so all denominations would feel welcome in Virginia and freely exercise their religious expression anywhere.
Jefferson’s use of the term "Separation of Church and State,” as had clergy for centuries, was to affirm the historic understanding government had no authority to stop, inhibit or regulate public religious expressions. The intended “separation wall” was one way, to keep government from interfering with the people’s religious expression but not restrict free religious expression in government.
Tony Patterson, Emmett