The Santa Barbara presidio (the Spanish fort) was built in 1782, four years before the mission. The mission was delayed because Governor Neve asked the Viceroy to withhold construction funds until the governor’s proposals for a reform of the mission system could be approved. He intended to implement these changes (which involved leaving the Indians in their villages and creating a smaller mission complex) beginning in Santa Barbara. By the time this was all resolved Neve was replaced by Pedro Fages and Fr. Serra had died.
The actual location of the mission was finally decided by Fr. Fermin Lasuen, Junipero Serra’s successor as Father President of the Mission chain. My understanding is that both Governor Neve and Fr. Serra thought that the mission should be on high ground at or near a site called Tanayan by the Indians and El Pedregoso by the Spaniards – the name in both languages means rocky mound, and the mission was built in this area. This location was an appropriate distance from the presidio (one and a half miles) and yes it did have a magnificent view of the valley, the presidio and the sea.
However, the exact location chosen for the mission was dictated largely because of its proximity to water resources, which the Spanish had learned was critical for the success of a mission. It seems quite logical to assume that the visibility of the mission from the sea might have been discussed but remember that the initial buildings were simple log structures.
The present imposing (and quite visible) church is actually the fourth church on the site, built between 1815-1820, almost forty years later.