The master branch of my firmware now has fully functioning bootloader code, which uses the Nordic nRF Connect app to flash the firmware. The configuration flash storage now also uses the pstorage module, and the device manager allows storage of bonding information. Unfortunately, while pstorage and the device manager were current in the SDK version 9 that the rbc_mesh requires, they are both deprecated in SDK12, which means once I can move up to the newest SDK, all that code will have to be replaced.
I also created a new repository, sdl-bootloader. This is required because the bootloader had to be recompiled with a setting to keep the configuration information stored in flash from being overwritten when new firmware is loaded. The #define, DFU_APP_DATA_RESERVED, is configured in dfu_types.h. I also removed a lot of the evaluation board specific buttons and leds from the bootloader code that I did not need.