regression in 3.1.0: docstring of ...:1:duplicate object description of ..., other instance in ..., use :noindex: for one of them

Describe the bug
Incompatibility with numpy docstring convention.

Attributes that are properties and have their own docstrings can be simply listed by name:
https://numpydoc.readthedocs.io/en/latest/format.html#class-docstring

To Reproduce
Toy example:

conf.py:

import os
import sys
import sphinx


CURR_PATH = os.path.abspath(os.path.dirname(__file__))
LIB_PATH = os.path.join(CURR_PATH, os.path.pardir, 'python-package')
sys.path.insert(0, LIB_PATH)


# -- General configuration ------------------------------------------------

# The master toctree document.
master_doc = 'index'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.autosummary',
    'sphinx.ext.todo',
    'sphinx.ext.viewcode',
    'sphinx.ext.napoleon',
]

autodoc_default_flags = ['members', 'inherited-members', 'show-inheritance']
autodoc_default_options = {
    "members": True,
    "inherited-members": True,
    "show-inheritance": True,
}

# Generate autosummary pages. Output should be set with: `:toctree: pythonapi/`
autosummary_generate = ['Python-API.rst']

# Only the class' docstring is inserted.
autoclass_content = 'class'

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False

index.rst:

.. toctree::
   :caption: Contents:

   Python API <Python-API>

Python-API.rst:

Python API
==========

.. currentmodule:: lightgbm


Scikit-learn API
----------------

.. autosummary::
    :toctree: pythonapi/

    A

..\python-package\lightgbm\sklearn.py:

class A(object):
    """Class A."""

    def __init__(self, x=42):
        """Init description.

        Parameters
        ----------
        x : int, optional (default=42)
            X description.

        Attributes
        ----------
        n_features_
        classes_ : array of shape = [n_classes]
            The class label array (only for classification problem).
        """
        self.x = x
        self._n_features = None
        self._n_classes = None


    @property
    def n_features_(self):
        """N features description."""
        return self._n_features

    @property
    def classes_(self):
        return 42

Expected behavior
No warnings.

Your project
https://github.com/microsoft/LightGBM/blob/master/docs/conf.py

Environment info

• OS: Linux and Win

• Python version: any

• Sphinx version: 3.1.0

• Sphinx extensions: in conf.py above

• Extra tools: -

• https://travis-ci.org/github/microsoft/LightGBM/jobs/696395266#L634

Start by reproducing the warning with the minimal conf.py, Python-API.rst, and sklearn.py example, using the listed autodoc, autosummary, and napoleon extensions. Trace how the class and its property docstrings are collected, then verify that the documented attributes no longer produce duplicate-object warnings while the property documentation remains available.