Compiler environments set CPPFLAGS and LDFLAGS with the include and library directory keys pointing to conda environment directories. However, some simple and non-standard makefiles and build scripts might not take these variables into account, which breaks virtualization of the compiler environment. However, there is another way to supply conda environment locations to the compiler - thorugh CPATH and LIBRARY_PATH environment variables which will be respected by the compilers directly, without any mediating script.
I have already started implementing this idea for [win] since it was not aligned with [unix] compilers in their ability to "virtualize" build environment for a compiler: #86