diff --git a/cmake/QtIRHelpers.cmake b/cmake/QtIRHelpers.cmake
index 3b20fa1e..7327ed18 100644
--- a/cmake/QtIRHelpers.cmake
+++ b/cmake/QtIRHelpers.cmake
@@ -102,6 +102,8 @@ endfunction()
 # into the final list of submodules to be included and excluded, which are then translated
 # to configure -submodules and -skip options.
 function(qt_ir_get_args_from_optfile_configure_filtered optfile_path out_var)
+    cmake_parse_arguments(arg "ALREADY_INITIALIZED" "" "" ${ARGV})
+
     # Get args unknown to init-repository, and pass them to configure as-is.
     qt_ir_get_unknown_args(unknown_args)
 
@@ -114,6 +116,9 @@ function(qt_ir_get_args_from_optfile_configure_filtered optfile_path out_var)
     qt_ir_get_option_value(module-subset submodules)
     if(submodules)
         qt_ir_get_top_level_submodules(include_submodules exclude_submodules)
+        if(NOT include_submodules AND arg_ALREADY_INITIALIZED)
+            set(include_submodules "${submodules}")
+        endif()
 
         # qtrepotools is always implicitly cloned, but it doesn't actually
         # have a CMakeLists.txt, so remove it.
diff --git a/cmake/QtTopLevelHelpers.cmake b/cmake/QtTopLevelHelpers.cmake
index c7058efb..1198771e 100644
--- a/cmake/QtTopLevelHelpers.cmake
+++ b/cmake/QtTopLevelHelpers.cmake
@@ -7,10 +7,14 @@ macro(qt_tl_include_all_helpers)
 endmacro()
 
 function(qt_tl_run_toplevel_configure top_level_src_path)
+    cmake_parse_arguments(arg "ALREADY_INITIALIZED" "" "" ${ARGV})
+
+    qt_ir_get_cmake_flag(ALREADY_INITIALIZED arg_ALREADY_INITIALIZED)
+
     # Filter out init-repository specific arguments before passing them to
     # configure.
-    qt_ir_get_args_from_optfile_configure_filtered("${OPTFILE}" configure_args)
-
+    qt_ir_get_args_from_optfile_configure_filtered("${OPTFILE}" configure_args
+        ${arg_ALREADY_INITIALIZED})
     # Get the path to the qtbase configure script.
     set(qtbase_dir_name "qtbase")
     set(configure_path "${top_level_src_path}/${qtbase_dir_name}/configure")
@@ -50,7 +54,7 @@ function(qt_tl_run_main_script)
     endif()
 
     # Then run configure out-of-process.
-    qt_tl_run_toplevel_configure("${TOP_LEVEL_SRC_PATH}")
+    qt_tl_run_toplevel_configure("${TOP_LEVEL_SRC_PATH}" ${exit_reason})
 endfunction()
 
 # Populates $out_module_list with all subdirectories that have a CMakeLists.txt file