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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 (!p_so.path.get_file().begins_with("lib")) {
		String err = "Android .so file names must start with \"lib\", but got: " + p_so.path;
		ERR_PRINT(err);
		return FAILED;
	}
	APKExportData *ed = static_cast<APKExportData *>(p_userdata);
	Vector<ABI> abis = get_abis();
	bool exported = false;
	for (int i = 0; i < p_so.tags.size(); ++i) {
		
		int abi_index = -1;
		for (int j = 0; j < abis.size(); ++j) {
			if (abis[j].abi == p_so.tags[i] || abis[j].arch == p_so.tags[i]) {
				abi_index = j;
				break;
			}
		}
		if (abi_index != -1) {
			exported = true;
			String abi = abis[abi_index].abi;
			String dst_path = String("lib").path_join(abi).path_join(p_so.path.get_file());
			Vector<uint8_t> array = FileAccess::get_file_as_bytes(p_so.path);
			Error store_err = store_in_apk(ed, dst_path, array);
			ERR_FAIL_COND_V_MSG(store_err, store_err, "Cannot store in apk file '" + dst_path + "'.");
		}