Setting the Blueprint Nativization Method to Exclusive while there are no blueprints present in the project, or selected causes this assertion.
I came across this bug attempting to verify another bug - UE-33021
Result: Package fails with Assertion
Expected Result: The package succeeds without error
UE4Editor_BlueprintCompilerCppBackend!FDependenciesGlobalMapHelper::GetDependenciesGlobalMap() blueprintcompilercppbackendutils.cpp:1921 UE4Editor_BlueprintCompilerCppBackend!FDependenciesGlobalMapHelper::EmitBodyCode() blueprintcompilercppbackendutils.cpp:1873 UE4Editor_BlueprintCompilerCppBackend!FBlueprintCompilerCppBackendModule::DependenciesGlobalMapBodyCode() blueprintcompilercppbackendmodule.cpp:85 UE4Editor_BlueprintNativeCodeGen!BlueprintNativeCodeGenUtilsImpl::GenerateNativizedDependenciesSourceFiles() blueprintnativecodegenutils.cpp:172 UE4Editor_BlueprintNativeCodeGen!FBlueprintNativeCodeGenUtils::FinalizePlugin() blueprintnativecodegenutils.cpp:277 UE4Editor_BlueprintNativeCodeGen!FBlueprintNativeCodeGenModule::FinalizeManifest() blueprintnativecodegenmodule.cpp:578 UE4Editor_UnrealEd!UCookOnTheFlyServer::CookByTheBookFinished() cookontheflyserver.cpp:5492 UE4Editor_UnrealEd!UCookOnTheFlyServer::TickCookOnTheSide() cookontheflyserver.cpp:2114 UE4Editor_UnrealEd!UCookCommandlet::NewCook() cookcommandlet.cpp:1582 UE4Editor_UnrealEd!UCookCommandlet::Main() cookcommandlet.cpp:868 UE4Editor_Cmd!FEngineLoop::PreInit() launchengineloop.cpp:2005 UE4Editor_Cmd!GuardedMain() launch.cpp:127 UE4Editor_Cmd!GuardedMainWrapper() launchwindows.cpp:130 UE4Editor_Cmd!WinMain() launchwindows.cpp:206 UE4Editor_Cmd!__scrt_common_main_seh() exe_common.inl:264 kernel32!<Unknown> ntdll!<Unknown>
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-40035 in the post.