### 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)
const String &prop_name = p_info.name;
	ERR_FAIL_COND(!props.has(prop_name));
	custom_prop_info[prop_name] = p_info;
}
const HashMap<StringName, PropertyInfo> &ProjectSettings::get_custom_property_info() const {
	return custom_prop_info;
}
bool ProjectSettings::is_using_datapack() const {
	return using_datapack;
}
bool ProjectSettings::is_project_loaded() const {
	return project_loaded;
}
bool ProjectSettings::_property_can_revert(const StringName &p_name) const {
	if (!props.has(p_name)) {
		return false;
	}
	return props[p_name].initial != props[p_name].variant;
}
bool ProjectSettings::_property_get_revert(const StringName &p_name, Variant &r_property) const {
	if (!props.has(p_name)) {
		return false;
	}
	
	r_property = props[p_name].initial.duplicate();
	return true;
}
void ProjectSettings::set_setting(const String &p_setting, const Variant &p_value) {