Found a solution. Because of subfolder having common names i decided to do the following:

1. Update the sys.path to only include these:

sys.path.insert(0, os.path.abspath('../../feature_service'))
sys.path.insert(0, os.path.abspath('../../feature_service/feature'))
## Exclude `extract` intentionally
#sys.path.insert(0, os.path.abspath('../../feature_service/extract'))

2. Update the sub-.rst files under extract/modules.rst to locate the directories properly, example adding a prefix extract. like following:

.. automodule:: extract.app_packages.v0_1.extract
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: extract.app_packages.v0_1
   :members:
   :undoc-members:
   :show-inheritance: