Нашел решение, которое сработало для меня:
# add the pch custom target as a dependency
add_dependencies(corelib pch)
# add the flag
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -include-pch ${CMAKE_CURRENT_BINARY_DIR}/stdinc.hpp.pch")
# target
add_custom_target(pch COMMAND clang -x c++-header ${CMAKE_CURRENT_SOURCE_DIR}/src/stdinc.hpp -o ${CMAKE_CURRENT_BINARY_DIR}/stdinc.hpp.pch)