diff --git a/packages/coding-agent/src/config/model-registry.ts b/packages/coding-agent/src/config/model-registry.ts
index 79a37904b..e97bb5737 100644
--- a/packages/coding-agent/src/config/model-registry.ts
+++ b/packages/coding-agent/src/config/model-registry.ts
@@ -839,26 +839,27 @@ export class ModelRegistry {
 		for (const customModel of customModels) {
 			const existingIndex = merged.findIndex(m => m.provider === customModel.provider && m.id === customModel.id);
 			if (existingIndex >= 0) {
+				const existingModel = merged[existingIndex];
 				merged[existingIndex] = enrichModelThinking({
-					...merged[existingIndex],
+					...existingModel,
 					id: customModel.id,
 					provider: customModel.provider,
 					api: customModel.api,
 					baseUrl: customModel.baseUrl,
-					name: customModel.name ?? merged[existingIndex].name,
-					reasoning: customModel.reasoning ?? merged[existingIndex].reasoning,
-					thinking: customModel.thinking ?? merged[existingIndex].thinking,
-					input: customModel.input ?? merged[existingIndex].input,
-					cost: customModel.cost ?? merged[existingIndex].cost,
-					contextWindow: customModel.contextWindow ?? merged[existingIndex].contextWindow,
-					maxTokens: customModel.maxTokens ?? merged[existingIndex].maxTokens,
-					headers: customModel.headers
-						? { ...merged[existingIndex].headers, ...customModel.headers }
-						: merged[existingIndex].headers,
-					compat: mergeCompat(merged[existingIndex].compat, customModel.compat),
-					contextPromotionTarget:
-						customModel.contextPromotionTarget ?? merged[existingIndex].contextPromotionTarget,
-					premiumMultiplier: customModel.premiumMultiplier ?? merged[existingIndex].premiumMultiplier,
+					name: customModel.name ?? existingModel.name,
+					reasoning: customModel.reasoning ?? existingModel.reasoning,
+					thinking: customModel.thinking ?? existingModel.thinking,
+					input: customModel.input ?? existingModel.input,
+					cost: customModel.cost ?? existingModel.cost,
+					contextWindow: customModel.contextWindow ?? existingModel.contextWindow,
+					maxTokens: customModel.maxTokens ?? existingModel.maxTokens,
+					// Same-id custom definitions replace bundled transport behavior. Provider-level
+					// headers/compat were already folded into customModel during parsing; do not
+					// re-merge bundled transport metadata here.
+					headers: customModel.headers,
+					compat: customModel.compat,
+					contextPromotionTarget: customModel.contextPromotionTarget ?? existingModel.contextPromotionTarget,
+					premiumMultiplier: customModel.premiumMultiplier ?? existingModel.premiumMultiplier,
 				} as Model<Api>);
 			} else {
 				merged.push(finalizeCustomModel(customModel, { useDefaults: true }));
diff --git a/packages/coding-agent/test/model-registry.test.ts b/packages/coding-agent/test/model-registry.test.ts
index c40cc8e92..2a2c1e3ec 100644
--- a/packages/coding-agent/test/model-registry.test.ts
+++ b/packages/coding-agent/test/model-registry.test.ts
@@ -322,6 +322,25 @@ describe("ModelRegistry", () => {
 			expect(sonnetModels[0].baseUrl).toBe("https://my-proxy.example.com/v1");
 		});
 
+		test("custom same-id replacement does not keep bundled headers", () => {
+			writeRawModelsJson({
+				"github-copilot": {
+					baseUrl: "https://proxy.example.com/v1",
+					headers: { "X-Proxy": "proxy" },
+					apiKey: "TEST_KEY",
+					api: "openai-completions",
+					models: [{ id: "gpt-4o" }],
+				},
+			});
+
+			const registry = new ModelRegistry(authStorage, modelsJsonPath);
+			const model = registry.find("github-copilot", "gpt-4o");
+
+			expect(model?.headers).toEqual({ "X-Proxy": "proxy" });
+			expect(model?.headers?.["User-Agent"]).toBeUndefined();
+			expect(model?.headers?.["Editor-Version"]).toBeUndefined();
+		});
+
 		test("custom provider with same name as built-in does not affect other built-in providers", () => {
 			writeModelsJson({
 				anthropic: providerConfig("https://my-proxy.example.com/v1", [{ id: "claude-custom" }]),
@@ -638,7 +657,7 @@ describe("ModelRegistry", () => {
 			expect(discovered?.headers?.["X-Model"]).toBeUndefined();
 		});
 
-		test("provider compat overlays preserve bundled model compat", () => {
+		test("same-id replacement uses configured compat without bundled compat leak", () => {
 			writeRawModelsJson({
 				"minimax-code": {
 					baseUrl: "https://proxy.example.com/v1",
@@ -653,8 +672,8 @@ describe("ModelRegistry", () => {
 
 			const registry = new ModelRegistry(authStorage, modelsJsonPath);
 			const model = registry.find("minimax-code", "MiniMax-M2.5");
-			expect(model?.compat?.thinkingFormat).toBe("zai");
-			expect(model?.compat?.reasoningContentField).toBe("reasoning_content");
+			expect(model?.compat?.thinkingFormat).toBeUndefined();
+			expect(model?.compat?.reasoningContentField).toBeUndefined();
 			expect(model?.compat?.extraBody).toEqual({ source: "proxy" });
 		});