diff --git a/e2e/cases/python-version-flag/test.sh b/e2e/cases/python-version-flag/test.sh
index c69b1cead..10143db02 100755
--- a/e2e/cases/python-version-flag/test.sh
+++ b/e2e/cases/python-version-flag/test.sh
@@ -36,3 +36,10 @@ for version in 3.9 3.10 3.11 3.12 3.13; do
         "--@rules_python//python/config_settings:python_version=${version}" \
         -- //python-version-flag:version_check "${version}"
 done
+
+# The native flag takes precedence over the legacy fallback when both are set.
+"$BAZEL" run \
+    --lockfile_mode=off \
+    --@aspect_rules_py//py:python_version=3.12 \
+    --@rules_python//python/config_settings:python_version=3.11 \
+    -- //python-version-flag:version_check 3.12
diff --git a/py/private/transitions.bzl b/py/private/transitions.bzl
index c81f1dc38..bb2fd4a04 100644
--- a/py/private/transitions.bzl
+++ b/py/private/transitions.bzl
@@ -19,9 +19,6 @@ def _baseline(settings, flag, current):
         return current
     return baseline
 
-def _python_version(settings):
-    return settings[PYTHON_VERSION_FLAG] or settings[_RPY_VERSION_FLAG]
-
 def _python_transition_impl(settings, attr):
     acc = {}
     acc[_PYTHON_VERSION_BASELINE_FLAG] = _baseline(
@@ -36,11 +33,14 @@ def _python_transition_impl(settings, attr):
     )
     if attr.python_version:
         version = str(attr.python_version)
+        acc[PYTHON_VERSION_FLAG] = version
+        acc[_RPY_VERSION_FLAG] = version
     else:
-        version = _python_version(settings)
-
-    acc[PYTHON_VERSION_FLAG] = version
-    acc[_RPY_VERSION_FLAG] = version
+        # No explicit pin: pass the flags through unchanged rather than
+        # writing a resolved value, which can flip them from unset/default
+        # and fork a new configuration for the whole transitive closure.
+        acc[PYTHON_VERSION_FLAG] = settings[PYTHON_VERSION_FLAG]
+        acc[_RPY_VERSION_FLAG] = settings[_RPY_VERSION_FLAG]
 
     # Set the dep_group transition. The attr is only present on `py_venv`
     # (rules without it propagate the inherited setting; `py_venv_exec`
diff --git a/py/tests/reset-data-edges/BUILD.bazel b/py/tests/reset-data-edges/BUILD.bazel
index 66176b2b5..033829a0f 100644
--- a/py/tests/reset-data-edges/BUILD.bazel
+++ b/py/tests/reset-data-edges/BUILD.bazel
@@ -1,5 +1,5 @@
 load("//py:defs.bzl", "py_binary", "py_library", "py_venv")
-load(":tests.bzl", "probe", "reset_data_edges_test_suite", "root", "terminal")
+load(":tests.bzl", "probe", "reset_data_edges_test_suite", "root", "seeded_root", "terminal")
 
 probe(name = "probe")
 
@@ -51,6 +51,12 @@ terminal(
     tags = ["manual"],
 )
 
+terminal(
+    name = "unversioned_terminal",
+    tags = ["manual"],
+    deps = [":probe"],
+)
+
 py_venv(
     name = "second",
     srcs = ["main.py"],
@@ -75,4 +81,12 @@ root(
     ],
 )
 
+seeded_root(
+    name = "seeded_root",
+    deps = [
+        ":probe",
+        ":unversioned_terminal",
+    ],
+)
+
 reset_data_edges_test_suite()
diff --git a/py/tests/reset-data-edges/tests.bzl b/py/tests/reset-data-edges/tests.bzl
index b24ada8c8..8f7f60e95 100644
--- a/py/tests/reset-data-edges/tests.bzl
+++ b/py/tests/reset-data-edges/tests.bzl
@@ -4,8 +4,11 @@ load("@bazel_skylib//lib:unittest.bzl", "analysistest", "asserts")
 load("//py/private:transitions.bzl", "python_transition", "reset_python_flags_transition")
 
 _DEP_GROUP_FLAG = "@aspect_rules_py//uv/private/constraints/dep_group:dep_group"
+_DEP_GROUP_BASELINE_FLAG = "@aspect_rules_py//uv/private/constraints/dep_group:baseline"
 _PYTHON_VERSION_FLAG = "@aspect_rules_py//py/private/interpreter:python_version"
+_PYTHON_VERSION_BASELINE_FLAG = "@aspect_rules_py//py/private/interpreter:baseline_python_version"
 _RPY_VERSION_FLAG = "@rules_python//python/config_settings:python_version"
+_RPY_VERSION_BASELINE_FLAG = "@aspect_rules_py//py/private/interpreter:baseline_rules_python_version"
 
 _ProbeInfo = provider(fields = ["file"])
 _ProbeFilesInfo = provider(fields = ["files"])
@@ -96,6 +99,45 @@ root = rule(
     },
 )
 
+# Give both dependency paths the same transition scratch state while preserving
+# the default/unset state of the version flags. An unpinned terminal used to
+# turn those version flags into explicit resolved values, creating a second
+# configured target for :probe.
+def _seed_baselines_transition_impl(settings, _attr):
+    return {
+        _DEP_GROUP_BASELINE_FLAG: settings[_DEP_GROUP_FLAG],
+        _PYTHON_VERSION_BASELINE_FLAG: settings[_PYTHON_VERSION_FLAG],
+        _RPY_VERSION_BASELINE_FLAG: settings[_RPY_VERSION_FLAG],
+    }
+
+_seed_baselines_transition = transition(
+    implementation = _seed_baselines_transition_impl,
+    inputs = [
+        _DEP_GROUP_FLAG,
+        _PYTHON_VERSION_FLAG,
+        _RPY_VERSION_FLAG,
+    ],
+    outputs = [
+        _DEP_GROUP_BASELINE_FLAG,
+        _PYTHON_VERSION_BASELINE_FLAG,
+        _RPY_VERSION_BASELINE_FLAG,
+    ],
+)
+
+seeded_root = rule(
+    implementation = _root_impl,
+    attrs = {
+        "deps": attr.label_list(
+            aspects = [_probe_aspect],
+            allow_empty = False,
+        ),
+        "_allowlist_function_transition": attr.label(
+            default = "@bazel_tools//tools/allowlists/function_transition_allowlist",
+        ),
+    },
+    cfg = _seed_baselines_transition,
+)
+
 def _reset_data_edges_test_impl(ctx):
     env = analysistest.begin(ctx)
     files = analysistest.target_under_test(env)[_ProbeFilesInfo].files.to_list()
@@ -114,3 +156,7 @@ def reset_data_edges_test_suite():
         name = "reset_data_edges_test",
         target_under_test = ":root",
     )
+    _reset_data_edges_test(
+        name = "unversioned_terminal_noop_transition_test",
+        target_under_test = ":seeded_root",
+    )