A dedicated group from St. John's and the Frederick County Historical Society answered this and several other questions tumbling about in the back of my mind in the book Burial Records St. John the Evangelist Church Frederick, Maryland From 1779 Through December 31, 2000. It turns out the Smiths and other early Frederick settlers were moved from their original graves at the Jesuit Novitiate graveyard when the Jesuits left Frederick in the early 20th century. Which FINALLY explains how Leonard Smith, who died in 1794 is buried in a cemetery that opened in 1845.
The book is drawn from church records recording deaths rather than actual burial records. As such, it includes people who were buried from St. John's but not at St. John's. It also includes at least two men not yet buried - my father-in-law and uncle, whose ashes await their very strong and long-lived wives. Long may they wait.