diff --git a/scripts/lib/native-value-e2e.mjs b/scripts/lib/native-value-e2e.mjs
index 88fba60cbf..a20ccb2e3a 100644
--- a/scripts/lib/native-value-e2e.mjs
+++ b/scripts/lib/native-value-e2e.mjs
@@ -253,20 +253,9 @@ async function verifyNativeValueAdapters(
       functionEvidence.analysis_profile,
     );
     assert.deepEqual(functionProfile, upstreamProfile);
-    const comparison = await client.callTool(
-      {
-        name: "compare_functions",
-        arguments: {
-          left: analyzed.structuredContent,
-          right: analyzed.structuredContent,
-        },
-      },
-      { timeout: 180000 },
-    );
-    assert.notEqual(comparison.isError, true, JSON.stringify(comparison));
-    assert.notEqual(comparison.structuredContent, undefined);
-    const comparisonEvidence = parseEvidence(
-      requireMcpOutput(comparison, "compare_functions"),
+    const comparisonEvidence = await compareRetainedFunctionEvidence(
+      client,
+      functionEvidence,
     );
     assert.equal(
       comparisonEvidence.normalized_result.status,
@@ -395,21 +384,27 @@ async function verifyUnresolvedCallEvidence(client) {
   assert.equal(trace.goal_status, "unknown");
   assert.equal(trace.truncated, true);
   assert.ok(trace.residual_unknowns.length > 0);
+  const compared = await compareRetainedFunctionEvidence(client, evidence);
+  assert.equal(compared.normalized_result.status, "unknown");
+}
+
+/** Compare an already admitted function record without retransmitting its payload. */
+export async function compareRetainedFunctionEvidence(client, evidence) {
+  const reference = {
+    kind: "retained-evidence",
+    evidence_id: evidence.evidence_id,
+  };
   const compared = await client.callTool(
     {
       name: "compare_functions",
       arguments: {
-        left: analyzed.structuredContent,
-        right: analyzed.structuredContent,
+        left: reference,
+        right: reference,
       },
     },
     { timeout: 180000 },
   );
   assert.notEqual(compared.isError, true, JSON.stringify(compared));
   assert.notEqual(compared.structuredContent, undefined);
-  assert.equal(
-    parseEvidence(requireMcpOutput(compared, "compare_functions"))
-      .normalized_result.status,
-    "unknown",
-  );
+  return parseEvidence(requireMcpOutput(compared, "compare_functions"));
 }
diff --git a/tests/boundary/process/nativeValueVerifierComparison.test.ts b/tests/boundary/process/nativeValueVerifierComparison.test.ts
new file mode 100644
index 0000000000..f73878257a
--- /dev/null
+++ b/tests/boundary/process/nativeValueVerifierComparison.test.ts
@@ -0,0 +1,102 @@
+import { fileURLToPath } from "node:url";
+import { expect } from "vitest";
+
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { processTest } from "../../support/process/processFixture.js";
+
+const moduleUrl = (path: string) =>
+  JSON.stringify(new URL(`../../../${path}`, import.meta.url).href);
+
+processTest.for([
+  { coverage: "complete", status: "unchanged" },
+  { coverage: "partial", status: "unknown" },
+] as const)(
+  "compares retained $coverage function Evidence within default MCP limits",
+  async ({ coverage, status }, { processes }) => {
+    const root = await createTestTempDirectory("rea-verifier-comparison-");
+    const source = `
+      import assert from "node:assert/strict";
+      import { writeFile } from "node:fs/promises";
+      import { join } from "node:path";
+      import { Client } from "@modelcontextprotocol/client";
+      import { StdioClientTransport } from "@modelcontextprotocol/client/stdio";
+      import { FUNCTION_COMPARISON_EXAMPLE } from ${moduleUrl("dist/contracts/functionComparisonExample.js")};
+      import { createEvidence } from ${moduleUrl("dist/domain/evidence.js")};
+      import { createEvidenceBundle } from ${moduleUrl("dist/domain/evidenceBundle.js")};
+      import { functionDossierSchema } from ${moduleUrl("dist/domain/native/functionDossier.js")};
+      import { compareRetainedFunctionEvidence } from ${moduleUrl("scripts/lib/native-value-e2e.mjs")};
+      import { requireMcpEvidenceBundle } from ${moduleUrl("scripts/lib/mcp-verifier-results.mjs")};
+
+      // Explicit synthetic facts qualify this adapter boundary, not real Ghidra.
+      const dossier = functionDossierSchema.parse(
+        structuredClone(FUNCTION_COMPARISON_EXAMPLE.left.normalized_result));
+      dossier.assembly = Array.from({ length: 1200 }, (_, i) => "synthetic instruction " + i);
+      const evidence = createEvidence({ path: "/synthetic/function.elf",
+        sha256: "a".repeat(64), format: "elf", architecture: "x86_64" },
+        { id: "synthetic-verifier-facts", name: "Explicit synthetic facts", version: "1" },
+        { operation: "analyze_function", parameters: { procedure: "main" }, result: dossier,
+          relationshipCoverage: { status: ${JSON.stringify(coverage)},
+            ...(${JSON.stringify(coverage)} === "partial"
+              ? { limitations: ["Explicit synthetic unresolved relationships."] } : {}) } });
+      const bundlePath = join(process.argv[1], "source.json");
+      await writeFile(bundlePath, JSON.stringify(createEvidenceBundle([evidence], [])));
+      const transport = new StdioClientTransport({ command: process.execPath,
+        args: [${JSON.stringify(fileURLToPath(new URL("../../../scripts/rea.mjs", import.meta.url)))}, "mcp"],
+        env: { PATH: process.env.PATH ?? "", REA_LOG_LEVEL: "silent",
+          HOPPER_LAUNCHER_PATH: "/rea-unconfigured-deep-provider/hopper" }, stderr: "pipe" });
+      const client = new Client({ name: "synthetic-verifier-comparison", version: "1" });
+      try {
+        await client.connect(transport);
+        const imported = await client.callTool({ name: "import_evidence_bundle",
+          arguments: { path: bundlePath } });
+        assert.notEqual(imported.isError, true, JSON.stringify(imported));
+        const inline = await client.callTool({ name: "compare_functions",
+          arguments: { left: evidence, right: evidence } });
+        assert.equal(inline.isError, true, JSON.stringify(inline));
+        const error = JSON.parse(inline.content.find(item => item.type === "text").text).error;
+        assert.equal(error.code, "resource_constraint");
+        assert.equal(error.details.reported_limits.max_input_elements, 1024);
+
+        // Execute the same request producer used by both real-provider controls.
+        const compared = await compareRetainedFunctionEvidence(client, evidence);
+        assert.equal(compared.normalized_result.status, ${JSON.stringify(status)});
+        assert.ok(compared.evidence_links.includes(evidence.evidence_id));
+        const bundle = requireMcpEvidenceBundle(await client.callTool({
+          name: "get_evidence_bundle", arguments: {} }));
+        for (const record of [evidence, compared])
+          assert.deepEqual(bundle.records.find(item => item.evidence_id === record.evidence_id), record);
+        const missingId = "ev_" + "b".repeat(64);
+        let missingFailure;
+        const checkedClient = { callTool: async (...args) => {
+          const reply = await client.callTool(...args);
+          assert.equal(reply.isError, true);
+          missingFailure = JSON.parse(reply.content.find(item => item.type === "text").text).error;
+          return reply;
+        } };
+        await assert.rejects(() => compareRetainedFunctionEvidence(checkedClient,
+          { ...evidence, evidence_id: missingId }), { name: "AssertionError" });
+        assert.equal(missingFailure.details.reason, "missing");
+        assert.equal(missingFailure.details.evidence_id, missingId);
+        assert.match(missingFailure.message, /not available from the selected source/);
+        console.log(JSON.stringify({ status: compared.normalized_result.status,
+          exact_source_link: true, complete_records_retained: true, missing_reference_refused: true }));
+      } finally {
+        await client.close();
+        await transport.close();
+      }
+    `;
+    const result = await processes.run(process.execPath, [
+      "--input-type=module",
+      "--eval",
+      source,
+      root,
+    ]);
+    expect(result.exitCode, `${result.stdout}\n${result.stderr}`).toBe(0);
+    expect(JSON.parse(result.stdout.trim())).toEqual({
+      status,
+      exact_source_link: true,
+      complete_records_retained: true,
+      missing_reference_refused: true,
+    });
+  },
+);