diff --git a/lib/python/base_cli/config.py b/lib/python/base_cli/config.py
index 2b9519a..25953e5 100644
--- a/lib/python/base_cli/config.py
+++ b/lib/python/base_cli/config.py
@@ -176,10 +176,22 @@ def _merge_mapping_validated(
         for existing_path in tuple(provenance):
             if existing_path == path or existing_path.startswith(f"{path}."):
                 del provenance[existing_path]
-        target[key] = dict(value) if isinstance(value, Mapping) else value
+        target[key] = _copy_config_value(value)
         provenance.update(_leaf_provenance(value, source, path))
 
 
+def _copy_config_value(value: Any) -> Any:
+    """Copy nested configuration containers without preserving YAML aliases."""
+
+    if isinstance(value, Mapping):
+        return {key: _copy_config_value(child) for key, child in value.items()}
+    if isinstance(value, list):
+        return [_copy_config_value(child) for child in value]
+    if isinstance(value, tuple):
+        return tuple(_copy_config_value(child) for child in value)
+    return value
+
+
 class BatteriesIncludedConfigLoader:
     """Load conventional user, project, environment, and explicit layers.
 
diff --git a/tests/test_batteries_included_config.py b/tests/test_batteries_included_config.py
index f65f03f..7880547 100644
--- a/tests/test_batteries_included_config.py
+++ b/tests/test_batteries_included_config.py
@@ -61,6 +61,11 @@ def test_shared_mapping_alias_is_valid_but_recursive_alias_is_rejected_with_path
         provenance: dict[str, str] = {}
         _merge_mapping(values, provenance, valid, "user")
         self.assertEqual(values, {"left": shared, "right": shared})
+        self.assertIsNot(values["left"], shared)
+        self.assertIsNot(values["left"], values["right"])
+        assert isinstance(values["left"], dict)
+        values["left"]["answer"] = 7
+        self.assertEqual(values["right"], {"answer": 42})
         self.assertEqual(provenance, {"left.answer": "user", "right.answer": "user"})
 
         with tempfile.TemporaryDirectory() as tmpdir:
@@ -69,6 +74,18 @@ def test_shared_mapping_alias_is_valid_but_recursive_alias_is_rejected_with_path
             with self.assertRaisesRegex(base_cli.ConfigurationError, "recursive.yaml.*recursive value.*nested.child"):
                 BatteriesIncludedConfigLoader(user_config_dir=Path(tmpdir) / "user").load(None, path)
 
+    def test_nested_mapping_aliases_are_isolated_across_layers(self) -> None:
+        shared = {"limits": {"retries": 2}}
+        values: dict[str, object] = {}
+        provenance: dict[str, str] = {}
+
+        _merge_mapping(values, provenance, {"first": shared, "second": shared}, "user")
+        _merge_mapping(values, provenance, {"first": {"limits": {"timeout": 30}}}, "project")
+
+        self.assertEqual(values["first"], {"limits": {"retries": 2, "timeout": 30}})
+        self.assertEqual(values["second"], {"limits": {"retries": 2}})
+        self.assertEqual(shared, {"limits": {"retries": 2}})
+
     def test_mapping_depth_is_bounded_before_recursive_merge_or_provenance(self) -> None:
         nested: dict[str, object] = {"value": 1}
         for index in range(65):