I visited San Francisco in 2017 and loved the Columbarium so much that it had to go in the book. I took some liberties with what it contains, but it is indeed kept in meticulous condition by Emmitt Watson, the cheerful African-American caretaker I met there. His office is filled with photos of visitors and he even has a comic about him, The Palace of Ashes, by Andy Warner.
The details of Mission Dolores are based on my visit there and it is true that Junípero Serra’s relics were dispersed based on donations. His canonization was contested by Native American groups but went ahead in September 2015. The journalist and historian, Carey McWilliams, described the Missions as ‘a series of picturesque charnel houses.’