diff --git a/spacy/tests/serialize/test_serialize_config.py b/spacy/tests/serialize/test_serialize_config.py
index 7d96c9063..d305d7719 100644
--- a/spacy/tests/serialize/test_serialize_config.py
+++ b/spacy/tests/serialize/test_serialize_config.py
@@ -420,7 +420,7 @@ def test_config_overrides_registered_functions():
     nlp.add_pipe("attribute_ruler")
     with make_tempdir() as d:
         nlp.to_disk(d)
-        nlp = spacy.load(
+        nlp_re1 = spacy.load(
             d,
             config={
                 "components": {
@@ -431,9 +431,26 @@ def test_config_overrides_registered_functions():
             },
         )
         assert (
-            nlp.config["components"]["attribute_ruler"]["scorer"]["@scorers"]
+            nlp_re1.config["components"]["attribute_ruler"]["scorer"]["@scorers"]
             == "spacy.tagger_scorer.v1"
         )
+        nlp_re2 = spacy.load(
+            d,
+            config={
+                "components": {
+                    "attribute_ruler": {
+                        "scorer": {
+                            "@scorers": "spacy.overlapping_labeled_spans_scorer.v1",
+                            "spans_key": "some_other_key",
+                        }
+                    }
+                }
+            },
+        )
+        assert (
+            nlp_re2.config["components"]["attribute_ruler"]["scorer"]["spans_key"]
+            == "some_other_key"
+        )
 
 
 def test_config_interpolation():
diff --git a/spacy/tests/test_misc.py b/spacy/tests/test_misc.py
index 618f17334..23a66263d 100644
--- a/spacy/tests/test_misc.py
+++ b/spacy/tests/test_misc.py
@@ -237,6 +237,10 @@ def test_minor_version(a1, a2, b1, b2, is_match):
             {"training.batch_size": 128, "training.optimizer.learn_rate": 0.01},
             {"training": {"batch_size": 128, "optimizer": {"learn_rate": 0.01}}},
         ),
+        (
+            {"attribute_ruler.scorer.@scorers": "spacy.tagger_scorer.v1"},
+            {"attribute_ruler": {"scorer": {"@scorers": "spacy.tagger_scorer.v1"}}},
+        ),
     ],
 )
 def test_dot_to_dict(dot_notation, expected):
@@ -245,6 +249,29 @@ def test_dot_to_dict(dot_notation, expected):
     assert util.dict_to_dot(result) == dot_notation
 
 
+@pytest.mark.parametrize(
+    "dot_notation,expected",
+    [
+        (
+            {"token.pos": True, "token._.xyz": True},
+            {"token": {"pos": True, "_": {"xyz": True}}},
+        ),
+        (
+            {"training.batch_size": 128, "training.optimizer.learn_rate": 0.01},
+            {"training": {"batch_size": 128, "optimizer": {"learn_rate": 0.01}}},
+        ),
+        (
+            {"attribute_ruler.scorer": {"@scorers": "spacy.tagger_scorer.v1"}},
+            {"attribute_ruler": {"scorer": {"@scorers": "spacy.tagger_scorer.v1"}}},
+        ),
+    ],
+)
+def test_dot_to_dict_overrides(dot_notation, expected):
+    result = util.dot_to_dict(dot_notation)
+    assert result == expected
+    assert util.dict_to_dot(result, for_overrides=True) == dot_notation
+
+
 def test_set_dot_to_object():
     config = {"foo": {"bar": 1, "baz": {"x": "y"}}, "test": {"a": {"b": "c"}}}
     with pytest.raises(KeyError):
diff --git a/spacy/util.py b/spacy/util.py
index ac38fbc90..9f1b886bf 100644
--- a/spacy/util.py
+++ b/spacy/util.py
@@ -511,7 +511,7 @@ def load_model_from_path(
     if not meta:
         meta = get_model_meta(model_path)
     config_path = model_path / "config.cfg"
-    overrides = dict_to_dot(config)
+    overrides = dict_to_dot(config, for_overrides=True)
     config = load_config(config_path, overrides=overrides)
     nlp = load_model_from_config(
         config,
@@ -1479,14 +1479,19 @@ def dot_to_dict(values: Dict[str, Any]) -> Dict[str, dict]:
     return result
 
 
-def dict_to_dot(obj: Dict[str, dict]) -> Dict[str, Any]:
+def dict_to_dot(obj: Dict[str, dict], *, for_overrides: bool = False) -> Dict[str, Any]:
     """Convert dot notation to a dict. For example: {"token": {"pos": True,
     "_": {"xyz": True }}} becomes {"token.pos": True, "token._.xyz": True}.
 
-    values (Dict[str, dict]): The dict to convert.
+    obj (Dict[str, dict]): The dict to convert.
+    for_overrides (bool): Whether to enable special handling for registered
+        functions in overrides.
     RETURNS (Dict[str, Any]): The key/value pairs.
     """
-    return {".".join(key): value for key, value in walk_dict(obj)}
+    return {
+        ".".join(key): value
+        for key, value in walk_dict(obj, for_overrides=for_overrides)
+    }
 
 
 def dot_to_object(config: Config, section: str):
@@ -1528,17 +1533,20 @@ def set_dot_to_object(config: Config, section: str, value: Any) -> None:
 
 
 def walk_dict(
-    node: Dict[str, Any], parent: List[str] = []
+    node: Dict[str, Any], parent: List[str] = [], *, for_overrides: bool = False
 ) -> Iterator[Tuple[List[str], Any]]:
-    """Walk a dict and yield the path and values of the leaves, treating
-    registered functions that start with @ as final values rather than dicts to
-    traverse."""
+    """Walk a dict and yield the path and values of the leaves.
+
+    for_overrides (bool): Whether to treat registered functions that start with
+        @ as final values rather than dicts to traverse.
+    """
     for key, value in node.items():
         key_parent = [*parent, key]
-        if isinstance(value, dict) and not any(
-            value_key.startswith("@") for value_key in value
+        if isinstance(value, dict) and (
+            not for_overrides
+            or not any(value_key.startswith("@") for value_key in value)
         ):
-            yield from walk_dict(value, key_parent)
+            yield from walk_dict(value, key_parent, for_overrides=for_overrides)
         else:
             yield (key_parent, value)