Add flag to not add top-level modules to PYTHONPATH

stub_template_host.txt added all the top-level modules to the
PYTHONPATH, which isn't correct, and caused absl.logging to
override the built-in logging module.

Removing this also makes it more consistent with python binaries
built with embedded_launcher: true. embedded_launcher: true
binaries don't add the top-level modules.

Fixes: 245583294
Test: m py_dont_add_top_level_dirs_test && out/host/linux-x86/testcases/py_dont_add_top_level_dirs_test/x86_64/py_dont_add_top_level_dirs_test
Change-Id: Id3069565d2b2c4b2bda0ff5301e757a7b4201751