In this case, the solution direction commented by @Tsyvarev was chosen.

• Instead of including the runner.c file a dependent library was linked.

• Each platform directory creates its own version of the platform runner library.

The following alterations have been made to the solution above.

# app-cpu1/CMakeLists.txt
add_executable(CPU1-app
  src/.. src files .ext
)
target_link_libraries(CPU1-app
    runnerLibrary
)

# target/platform/CMakeLists.txt

add_library(runnerLibrary STATIC
    src/runner.c
)
target_include_directories(runnerLibrary PRIVATE
    additional/include/directories)
target_link_libraries(runnerLibrary PRIVATE
    additional/link/libraries)

This solution made more sense that the initial proposed solution in the question:

1. Dependencies are more clear, that they are on a specific library rather than a file.

2. Library dependencies can be made clear rather than single file dependencies.