Our SCons implementation offers a --variables-files flag which can be used to specify one or more files to load.
Most often, it is used to name a file that describes how to use the custom MongoDB toolchain.
Once you have named that file, SCons will assume that it means that you didn't want to load your personal mongo_custom_variables.py from $HOME/.scons/site_scons.
In order to do both things, you need to pass both files as arguments, wrapped in quotes, like --variables-files="$HOME/.scons/site_scons/mongo_custom_variables.py ./etc/scons/icecream_macosx_via_linux_cross.vars". This is fragile and annoying.
We should improve the UX for this, so that it is easier for users to both name a toolchain, and record customizations in their personal variables files, such as providing a developer friendly generator for the MONGO_VERSION variable, or enabling icecream or ccache.