Config file: system_site_packages overwritten from project's setting

I created a test case to demostrate what was reported in the issue. Summarizing,
if the project uses a config file and does not define `python.system_packages`
but has `Project.use_system_packages=True` the config option is `True` which is
wrong. When a config file is used, settings at Project level should be ignored
as this messages from "Advanced settings" states:

> These settings can be configured using a configuration file. That's the
recommended way to set up your project. Settings listed here are ignored when
using a configuration file.

Reference #8782

Author: humitos

readthedocs/rtd_tests/tests/test_config_integration.py

@@ -767,6 +767,38 @@ def test_system_packages(self, run, checkout_path, tmpdir):
         assert '--system-site-packages' in args
         assert config.python.use_system_site_packages
 
+    @patch('readthedocs.doc_builder.environments.BuildEnvironment.run')
+    def test_system_packages_project_overrides(self, run, checkout_path, tmpdir):
+
+        # Define `project.use_system_packages` as if it was marked in the Advanced settings.
+        self.version.project.use_system_packages = True
+        self.version.project.save()
+
+        checkout_path.return_value = str(tmpdir)
+        self.create_config_file(
+            tmpdir,
+            {
+                # Do not define `system_packages: True` in the config file.
+                'python': {},
+            },
+        )
+
+        update_docs = self.get_update_docs_task()
+        config = update_docs.config
+
+        python_env = Virtualenv(
+            version=self.version,
+            build_env=update_docs.build_env,
+            config=config,
+        )
+        update_docs.python_env = python_env
+        update_docs.python_env.setup_base()
+
+        args, kwargs = run.call_args
+
+        assert '--system-site-packages' not in args
+        assert not config.python.use_system_site_packages
+
     @pytest.mark.parametrize(
         'value,result',
         [