I figured it out. The flag '-framework Cocoa` is a flag for the linker. To get it passed to the linker one has to append LINKFLAGS to the SCons environment. For this I created an extra_script (saved in the same folder as platform.ini):
file: pre_extra_script.py
Import("env")
env.Append(LINKFLAGS=['-framework', 'Cocoa'])
and make sure it gets executed before the build starts by adding it to the platform.ini file.
file: platform.ini
[env:native]
platform = native
extra_scripts = pre:pre_extra_script.py
No additional build_flags are necessary.