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***Bugsquad note:** This issue has been confirmed several times already. No need to confirm it further.*

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### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Ubuntu 22.04

### Issue description

I followed this tutorial
https://docs.godotengine.org/en/stable/tutorials/export/android_custom_build.html#doc-android-custom-build.

I want to create Android launcher app to do this i added following code to AndroidManifest.xml in Android Studio.
`<category android:name="android.intent.category.HOME" />
<category android:name="android.intent.category.DEFAULT" />`

But when I export APK my modifications are removed from AndroidManifest.xml.


### Steps to reproduce

Followed this tutorial
https://docs.godotengine.org/en/stable/tutorials/export/android_custom_build.html#doc-android-custom-build.

then open android project in Android studio and edit AndroidManifest.xml.

### Minimal reproduction project

N/A

if (!apk_expansion) {
			print_verbose("Exporting project files...");
			CustomExportData user_data;
			user_data.assets_directory = assets_directory;
			user_data.debug = p_debug;
			if (p_flags & DEBUG_FLAG_DUMB_CLIENT) {
				err = export_project_files(p_preset, p_debug, ignore_apk_file, &user_data, copy_gradle_so);
			} else {
				err = export_project_files(p_preset, p_debug, rename_and_store_file_in_gradle_project, &user_data, copy_gradle_so);
			}
			if (err != OK) {
				add_message(EXPORT_MESSAGE_ERROR, TTR("Export"), TTR("Could not export project files to gradle project."));
				return err;
			}
			if (user_data.libs.size() > 0) {
				Ref<FileAccess> fa = FileAccess::open(GDEXTENSION_LIBS_PATH, FileAccess::WRITE);
				fa->store_string(JSON::stringify(user_data.libs, "\t"));
			}
		} else {
			print_verbose("Saving apk expansion file...");
			err = save_apk_expansion_file(p_preset, p_debug, p_path);
			if (err != OK) {
				add_message(EXPORT_MESSAGE_ERROR, TTR("Export"), TTR("Could not write expansion package file!"));
				return err;
			}
		}
		print_verbose("Storing command line flags...");
		store_file_at_path(assets_directory + "/_cl_", command_line_flags);
		print_verbose("Updating ANDROID_HOME environment to " + sdk_path);
		OS::get_singleton()->set_environment("ANDROID_HOME", sdk_path);