The important part is whether Adafruit SPIFlash appears in the Dependency graph outputted at the start of compilation. What does it look like? The libraries may be generally declared but if the library dependency finder (LDF) doesn’t detect its usage, it won’t be included in the build process properly.
Doing a #include <Adafruit_SPIFlash.h> in the src/main.cpp file might also solve your problem.