### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
};
void ProjectSettings::_get_property_list(List<PropertyInfo> *p_list) const {
	_THREAD_SAFE_METHOD_
	RBSet<_VCSort> vclist;
	for (const KeyValue<StringName, VariantContainer> &E : props) {
		const VariantContainer *v = &E.value;
		if (v->hide_from_editor) {
			continue;
		}
		_VCSort vc;
		vc.name = E.key;
		vc.order = v->order;
		vc.type = v->variant.get_type();
		if (v->internal || vc.name.begins_with("input/") || vc.name.begins_with("importer_defaults/") || vc.name.begins_with("import/") || vc.name.begins_with("autoload/") || vc.name.begins_with("editor_plugins/") || vc.name.begins_with("shader_globals/")) {
			vc.flags = PROPERTY_USAGE_STORAGE;
		} else {