From the issue you link, It looks like this is due to trying to use toolbox to run python on coreos. I believe this is due to having a shell script at /opt/bin/python that tries to execute /usr/bin/python inside of the toolbox container:
core@coreos ~ $ /opt/bin/python -c 'import sys; print sys.executable'
/usr/bin/python
I believe that is the problem where the reports of "No such file or directory" are coming from. The "python" path on the coreos machine is in a different location than the actual python binary in the toolbox container, so when `/opt/bin/python` is executed in the container, it fails.
In a simple test to see if this could be resolved, I linked /usr/bin/python to /opt/bin/python inside the toolbox container, and it resolves the issues:
$ toolbox --quiet /bin/sh
/bin/sh: can't access tty; job control turned off
/ # mkdir -p /opt/bin
/ # ln -s /usr/bin/python /opt/bin/
As for python being able to use a zipped file for imports, that is built in functionality of python: