I just visual traced the code and it looks to me that "Build file" does not use the custom makefile.
From compilergcc.cpp line 3133 current SVN
return CompileFileDefault(m_pProject, pf, bt); // compile file using default build system
Edit: Adding the use of "UseMake" call in compilergcc.cpp would be a partial fix; but, other than adding an error saying not supported I have no idea what to add without a lot more work.
Tim S.