diff --git a/scripts/generate-npm-shrinkwrap.mjs b/scripts/generate-npm-shrinkwrap.mjs
index 2691145c1f38..3044c45f8e52 100644
--- a/scripts/generate-npm-shrinkwrap.mjs
+++ b/scripts/generate-npm-shrinkwrap.mjs
@@ -305,11 +305,60 @@ function mergeOverrideEntry(merged, name, spec) {
     }
     return;
   }
+  if (
+    typeof current === "string" &&
+    isPlainObject(spec) &&
+    typeof spec["."] === "string" &&
+    exactOverrideVersionsMatch(current, spec["."])
+  ) {
+    merged[name] = { ".": preferredExactOverrideRootSpec(current, spec["."]) };
+    for (const [nestedName, nestedSpec] of Object.entries(spec)) {
+      if (nestedName === ".") {
+        continue;
+      }
+      mergeOverrideEntry(merged[name], nestedName, nestedSpec);
+    }
+    return;
+  }
+  if (
+    isPlainObject(current) &&
+    typeof spec === "string" &&
+    typeof current["."] === "string" &&
+    exactOverrideVersionsMatch(current["."], spec)
+  ) {
+    current["."] = preferredExactOverrideRootSpec(current["."], spec);
+    return;
+  }
   if (JSON.stringify(current) !== JSON.stringify(spec)) {
     throw new Error(`package.json overrides.${name} conflicts with pnpm lock policy for ${name}`);
   }
 }
 
+function preferredExactOverrideRootSpec(current, incoming) {
+  return incoming.startsWith("npm:") ? incoming : current;
+}
+
+function exactOverrideVersionsMatch(left, right) {
+  const leftVersion = exactVersionFromOverrideSpec(left);
+  if (leftVersion === null || leftVersion !== exactVersionFromOverrideSpec(right)) {
+    return false;
+  }
+  const leftAlias = parseNpmAliasOverrideSpec(left);
+  const rightAlias = parseNpmAliasOverrideSpec(right);
+  return !leftAlias || !rightAlias || leftAlias.name === rightAlias.name;
+}
+
+function parseNpmAliasOverrideSpec(spec) {
+  if (!spec.startsWith("npm:")) {
+    return null;
+  }
+  const versionIndex = spec.lastIndexOf("@");
+  if (versionIndex <= "npm:".length) {
+    return null;
+  }
+  return { name: spec.slice("npm:".length, versionIndex) };
+}
+
 function mergeOverrides(packageOverrides, workspaceOverrides, pnpmLockOverrides) {
   const merged = normalizeOverrides(packageOverrides);
   for (const [name, spec] of [
@@ -1085,6 +1134,7 @@ export {
   disableShrinkwrappedOverrideConflictSources,
   exactOverrideRulesFromOverrides,
   exactVersionFromOverrideSpec,
+  mergeOverrides,
   applyPackageExtensionPeerMetadata,
   normalizeNpmVersionDrift,
   packageJsonForShrinkwrap,
diff --git a/test/package-manager-config.test.ts b/test/package-manager-config.test.ts
index ec65d8e75387..149f908f3ca6 100644
--- a/test/package-manager-config.test.ts
+++ b/test/package-manager-config.test.ts
@@ -4,6 +4,7 @@ import { parse } from "yaml";
 import {
   collectCurrentShrinkwrapOverrides,
   collectPnpmLockViolations,
+  mergeOverrides,
   parsePnpmPackageKey,
   readShrinkwrapOverrides,
 } from "../scripts/generate-npm-shrinkwrap.mjs";
@@ -132,6 +133,82 @@ describe("package manager build policy", () => {
     });
   });
 
+  it("merges exact current shrinkwrap pins with nested lock-derived pins", () => {
+    expect(
+      mergeOverrides(
+        { "@mistralai/mistralai": "2.2.1" },
+        { "@mistralai/mistralai": { ".": "2.2.1", zod: "4.4.3" } },
+        {},
+      ),
+    ).toEqual({
+      "@mistralai/mistralai": { ".": "2.2.1", zod: "4.4.3" },
+    });
+  });
+
+  it("preserves npm alias pins when merging nested lock-derived pins", () => {
+    expect(
+      mergeOverrides(
+        { "node-domexception": "npm:@nolyfill/domexception@1.0.28" },
+        { "node-domexception": { ".": "1.0.28", child: "2.0.0" } },
+        {},
+      ),
+    ).toEqual({
+      "node-domexception": {
+        ".": "npm:@nolyfill/domexception@1.0.28",
+        child: "2.0.0",
+      },
+    });
+  });
+
+  it("preserves later npm alias pins when nested pins are already merged", () => {
+    expect(
+      mergeOverrides(
+        { "node-domexception": { ".": "1.0.28", child: "2.0.0" } },
+        { "node-domexception": "npm:@nolyfill/domexception@1.0.28" },
+        {},
+      ),
+    ).toEqual({
+      "node-domexception": {
+        ".": "npm:@nolyfill/domexception@1.0.28",
+        child: "2.0.0",
+      },
+    });
+  });
+
+  it("rejects non-exact root pins when merging nested pins", () => {
+    expect(() =>
+      mergeOverrides(
+        { "floating-package": "^1.0.0" },
+        { "floating-package": { ".": "~1.0.0", child: "2.0.0" } },
+        {},
+      ),
+    ).toThrow(/conflicts with pnpm lock policy/u);
+    expect(() =>
+      mergeOverrides(
+        { "floating-package": { ".": "^1.0.0", child: "2.0.0" } },
+        { "floating-package": "~1.0.0" },
+        {},
+      ),
+    ).toThrow(/conflicts with pnpm lock policy/u);
+  });
+
+  it("rejects distinct npm alias targets with matching versions", () => {
+    expect(() =>
+      mergeOverrides(
+        { "aliased-package": "npm:@safe/foo@1.0.0" },
+        { "aliased-package": { ".": "npm:@other/foo@1.0.0", child: "2.0.0" } },
+        {},
+      ),
+    ).toThrow(/conflicts with pnpm lock policy/u);
+    expect(() =>
+      mergeOverrides(
+        { "aliased-package": { ".": "npm:@safe/foo@1.0.0", child: "2.0.0" } },
+        { "aliased-package": "npm:@other/foo@1.0.0" },
+        {},
+      ),
+    ).toThrow(/conflicts with pnpm lock policy/u);
+  });
+
   it("keeps npm shrinkwrap package versions inside the pnpm lock graph", () => {
     const pnpmLockPackages = collectPnpmLockPackages();
     const shrinkwrapPaths = [