The CMake build scripts don't use the flags provided by CMAKE_Fortran_FLAGS and friends when building. This makes it difficult to rebuild with tweaked compiler flags, as changes have to be added to the CMakeLists.txt in the source tree.
Expected behavior:
The CMake build should use (or at least append) the standard CMake compiler flags when compiling Fortran code
Workaround
Make temporary changes to CMakeLists.txt in the source tree to add debug flags, etc.