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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

String manifest_xr_features;
	int xr_mode_index = (int)(p_preset->get("xr_features/xr_mode"));
	bool uses_xr = xr_mode_index == XR_MODE_OPENXR;
	if (uses_xr) {
		int hand_tracking_index = p_preset->get("xr_features/hand_tracking"); 
		if (hand_tracking_index == XR_HAND_TRACKING_OPTIONAL) {
			manifest_xr_features += "    <uses-feature tools:node=\"replace\" android:name=\"oculus.software.handtracking\" android:required=\"false\" />\n";
		} else if (hand_tracking_index == XR_HAND_TRACKING_REQUIRED) {
			manifest_xr_features += "    <uses-feature tools:node=\"replace\" android:name=\"oculus.software.handtracking\" android:required=\"true\" />\n";
		}
		int passthrough_mode = p_preset->get("xr_features/passthrough");
		if (passthrough_mode == XR_PASSTHROUGH_OPTIONAL) {
			manifest_xr_features += "    <uses-feature tools:node=\"replace\" android:name=\"com.oculus.feature.PASSTHROUGH\" android:required=\"false\" />\n";
		} else if (passthrough_mode == XR_PASSTHROUGH_REQUIRED) {
			manifest_xr_features += "    <uses-feature tools:node=\"replace\" android:name=\"com.oculus.feature.PASSTHROUGH\" android:required=\"true\" />\n";
		}
	}
	if (p_uses_vulkan) {
		manifest_xr_features += "    <uses-feature tools:node=\"replace\" android:name=\"android.hardware.vulkan.level\" android:required=\"false\" android:version=\"1\" />\n";
		manifest_xr_features += "    <uses-feature tools:node=\"replace\" android:name=\"android.hardware.vulkan.version\" android:required=\"true\" android:version=\"0x400003\" />\n";
	}
	return manifest_xr_features;
}
String _get_activity_tag(const Ref<EditorExportPreset> &p_preset, bool p_uses_xr) {