The question references "Mission San Rafael Arcángel"—which does exist, but the phrasing suggests uncertainty. Let's set the record straight.
Mission San Rafael Arcángel was the 20th of 21 Spanish missions in Alta California, founded December 14, 1817, by Father Vicente de Sarria as a asistencia (sub-mission) of Mission San Francisco de Asís (Mission Dolores). It became a full mission in 1822. Located in present-day San Rafael, Marin County, North Bay.
Padres taught Catholicism, Spanish, agriculture (wheat, corn, grapes, olives), ranching, weaving, carpentry, and masonry. The mission eventually held 1,000+ neophytes, 20,000+ livestock, and extensive orchards/vineyards.
Land granted to Mexican Californios; mission buildings decayed. The current church (1949) is a replica on the original site. A small museum displays artifacts.
So yes—Mission San Rafael Arcángel is real, and its founding purpose was uniquely medical-strategic as well as spiritual.