> if you have entry points installed then moving them to another 
> machine would break their shebang lines.

Not if you port it on the same OS using, for example

#!/usr/bin/env python3

> And even if you do it on your local machine there's no guarantee
> something else wasn't structured to be directory-specific.

You are telling about user code, not the virtualenv itself. If the user doe not write the code in such a way it's portable, it's his fault. But this should not stop people that do it right to try to port the venv if possible.

I think the modification
VIRTUAL_ENV="$(dirname "$(dirname "$(readlink -nf "$0")")")"

is very little and quite robust. Don't know how to do in fish and csh shells, but in bash and sh it works.