I may have answered my own question: If I modify the setup.py to use:
packages = find_packages(),
and change the directory structure to:
...
|-package1
| |-setup.py
| |-MANIFEST.in
| |-com (symlink to ../com)
| |-utilities (symlink to ../utilities)
| |-package1
| | |-__init__.py
| | |-package1_1.py
| | |-package1_2.py
| | |-...
If I then cd into package1 and do:
% python setup.py sdist
It seems to create the distribution correctly.
Rob